Diagnosis and treatment of viral diseases

ABSTRACT

Provided are methods of diagnosing a viral disease such as idiopathic pulmonary fibrosis, Castleman&#39;s disease, a lymphoma, a thymoma or a sarcoma in a patient by identifying one or more virus-specific elements such as a nucleic acid or a viral protein or a patient antibody to a virus-specific element, as well as to kits for diagnosing the viral disease in a patient. Further provided are methods of monitoring disease progression and/or the efficacy of therapy by measuring the levels of a virus-specific element in a sample from a patient, and methods of identifying therapeutic agents that show efficacy in reducing levels of virus-specific agents in vitro. Still further provided are methods of treating idiopathic pulmonary fibrosis, a lymphoproliferative disease and cancer, as well as to methods of preventing viral infection, including Herpesvirus saimiri infection.

1. CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.15/897,217, filed Feb. 15, 2018, which is a continuation of U.S. patentapplication Ser. No. 15/439,495, now U.S. Pat. No. 9,933,427, issued onApr. 3, 2018, which is a continuation of U.S. patent application Ser.No. 14/759,687, now U.S. Pat. No. 9,617,607, issued Apr. 11, 2017, whichis a National Stage Entry of PCT/US14/10675, filed Jan. 8, 2014, whichis a continuation-in-part of U.S. patent application Ser. No.14/080,644, filed Nov. 14, 2013, now abandoned, which is acontinuation-in-part of U.S. patent application Ser. No. 13/920,964,filed Jun. 18, 2013, now abandoned, which claims the benefit under 35U.S.C. § 119(e) of U.S. Provisional Application No. 61/750,104, filedJan. 8, 2013, the contents of all of which are incorporated herein intheir entirety by reference thereto.

2. REFERENCE TO SEQUENCE LISTING, TABLE OR COMPUTER PROGRAM

The instant application contains a Sequence Listing which has beensubmitted electronically in ASCII format and is hereby incorporated byreference in its entirety. Said ASCII copy, created on Feb. 15, 2018, isnamed ENZ-109-CIP2-CON-CON-CON-SL.txt and is 13,413 bytes in size.

Herpesviruses are a family of very large double stranded DNA virusesranging from 125 KB to 240 KB in length. See, e.g., Davison A J.Comparative analysis of the genomes. In: Arvin et al., editors. HumanHerpesviruses: Biology, Therapy, and Immunoprophylaxis. (Cambridge:Cambridge University Press; 2007) Chapter 2. Available from:http://www.ncbi.nlm.nih.gov/books/NBK47439. Phylogenetically theHerpesvirus family is divided into three groups: α, β and γ. Althoughinitially grouped on the basis of different cell tropisms and biologicalproperties, further studies have shown that nucleic acid sequencedivergence also separates these groups of Herpesviruses. α-Herpesvirusesthat are known to infect humans are Herpes simplex 1 (HSV1), Herpessimplex 2 (HSV2) and Herpes zoster (VSV), the causative agent of bothchicken pox and shingles. A representative human pathogen of theβ-Herpesviruses is human Cytomegalovirus (CMV). The third group, theγ-Herpesviruses, are divided into two subgroups, Lymphocryptovirus andRhadinovirus. An example of the former is Epstein Barr Virus (EBV),which causes mononucleosis and certain lymphomas, and examples of thelatter are Herpesvirus saimiri (HVS), a monkey virus, MHV68 (a mousevirus) and human Herpesvirus 8 (HHV8, KSHV), which is associated withthe development of Kaposi's sarcoma. Herpesvirus infections areassociated with a “latent” period in which the virus is dormant for longperiods between activations. Certain cell types, such as neurons,B-cells and T-cells are associated with the latent virus. The HVS virusis endemic but nonpathogenic in squirrel monkeys. HVS infection of othermonkey species induces lymphomas, and in vitro infection of humanT-cells can lead to cellular transformation. See Biesinger et al. (1992)Proc. Nat Acad. Sci (USA) 89; 3116-3119. HVS itself has been furthersubdivided into three groups: A, B and C, but the differences are basedstrictly on a small region in the left end of the viral genomeresponsible for transformation (Medveczky et al., 1984 J. Virol. 52;938-944) while strong conservatism is seen within the sequences of therest of the genomes of each group. See Ensser et al. (2003) Virology314:471-487. Although HVS infection in humans was known (Ablashi et al.(1988) Intervirology 29(4):217-226), until the present disclosure, therewas no evidence that HVS could induce disease in humans. See Estep etal. (2010) Vaccine 285; 878-884.

Idiopathic pulmonary fibrosis (“IPF”) is a specific form of chronic,progressive fibrosing interstitial pneumonia of unknown cause thattypically presents in adults over 50 years of age. The characteristichistology of IPF includes sub-pleural fibrosis with many alveolar-basedsites of fibroblast proliferation and dense scarring, alternating withareas of normal lung tissue. Scattered interstitial inflammation occurswith lymphocyte, plasma cell, and macrophage and/or dendritic cellinfiltration. Honeycombing—lung fibrosis characterized by multiplecystic spaces located at the bases of the lungs—occurs in all patientsand increases with advanced disease. The result is deterioratingrespiratory function and death from respiratory failure. For recentreviews on this disease see Raghu et al. (2011) Am. J. Respir. Crit.Care Med. 183:788-824 and Noble et al. (2012) J. Clin. Invest. 122;2756-2762.

Symptoms and signs of IPF typically develop over 6 months to severalyears and include shortness of breath upon physical exertion (dyspnea),non-productive cough, bibasilar inspiratory (Velcro) crackles on chestexamination, and in some patients, clubbing of the fingers. However, IPFmay be misdiagnosed because its symptoms are similar to those of morecommon diseases, such as bronchitis, asthma and heart failure.Currently, diagnosis of IPF requires at least high-resolution computedtomography (HRTC), and may also include pulmonary function tests and/orsurgical lung biopsy. See Raghu (2011).

Most patients have moderate to advanced clinical disease at the time ofdiagnosis. Normal partial pressure of oxygen in arterial blood and fewerfibroblastic foci on biopsy at presentation predict a better prognosis,while advanced age, poor pulmonary function at presentation and severedyspnea predict a worse prognosis. Although some patients demonstrate agradual progression of the disease and others have an accelerateddecline, the clinical course eventually leads to death, with the mediansurvival being less than 3 years from diagnosis.

Over the years, efforts have been made to identify treatments to reverseor halt the progression of IPF. For example, the similarity of IPF toautoimmune diseases has led to attempts to treat IPF usingimmunomodulatory compounds, e.g., corticosteroids, etanercept and thelike, which were not proven to be effective and, indeed, may worsen thesymptomatology. See Papiris et al. (2012) Am. J. Respiratory and CritCare Med 185(5):587-588. Other pharmacological therapies that proved tobe ineffective have included, e.g., anticoagulants, phosphodiesteraseinhibitors, and mucolytic agents. See, e.g., Adamli et al. (2012) DrugDesign, Development and Therapy 6; 261-272; Cottin (2012) Eur Respir.Rev 21; 124, 161-167; Rafli et al., (2013) J Thoracic Dis. 5; 48-73.

The efforts to develop therapies for IPF have been largely unsuccessful,in part because the cause of the disease was not known. Accordingly,therapies have been aimed at treatment of certain complications andcomorbid conditions (e.g., pulmonary hypertension and/or asymptomaticgastroesophageal reflux), supportive therapies such as oxygen therapyfor hypoxemia, pulmonary rehabilitation and antibiotics for pneumonia,and therapies directed to easing the debilitating fibroticmanifestations of IPF. The drastic nature of the disease is reflected bythe fact that in some cases, lung transplantation for otherwise healthyIPF patients is recommended.

Attempts to elucidate the underlying cause of IPF have led to the searchfor markers, e.g., differences in protein and/or mRNA expression thatmight distinguish patients with IPF from normal subjects and/or patientswith other pulmonary diseases. Certain protein profiling studies ofpatients with IPF compared to normal controls have shown a lack ofsignificant differences between patients and controls in expression ofinflammatory markers, e.g., IL-17A, IL-23, RANTES. See Stin et al.(2013) Ann Thoracic Med. 8; 38-45; Ebina et al. (2011) PulmonaryMedicine Article ID 916486. Another study of in situ expression ofcytokines surprisingly showed high levels of expression of IL-17 inactively growing lung epithelial cells in IPF patients, which type ofcell was not previously associated with IL-17 expression. See Nuovo etal. (2012) Mod. Pathol. 25; 416-433.

Viruses have also been investigated as potential causative agents ofIPF. A number of different Herpesvirus types have been identified asbeing present in the lungs of IPF patients, and antibodies toHerpesviruses have been found in IPF patients. These Herpesvirusesinclude Herpes simplex 1 (HSV1), cytomegalovirus (CMV) (antibodies),human herpes virus 8 (HHV8) and Epstein Barr Virus (EBV), which appearedto be strongly associated with IPF. See, e.g., Yonemaru et al. (1997)Eur Resp J 10:2040-45; Magro et al. (2003) Am J Clin Pathol.119:556-567; Egan et al. (1995) Thorax 50:510-513; Stewart et al. (1999)Am J. Resp. Crit. Care Med. 159:1336-41; Tang et al., 2003 J. Clin.Microbiol. 41; 2633-2640. A further problem with assigning EBV as acausative factor is that by the age of 10, 95% of the population hasbeen infected by EBV. See Kutok et al. (2006) Annu. Rev. Pathol.375-404. As such, even if there were a connection between EBV and IPF,detection of EBV in a clinical sample has little predictive ordiagnostic value. Thus, it has been difficult to establish a consistentcorrelation between the presence of a particular Herpesvirus type andIPF in humans. See, e.g., Zamo et al. (2004) Sarcoidosis vasculitis andDiffuse Lung Diseases 22; 123-128 (failure to detect EBV in IPFpatients); Woolton et al. (2011) Am J. Resp. Crit. Care Med.183:1698-1702 (finding HSV in only 1/43 samples and EBV in 2/43 samplesfrom IPF patients); Dworniczak et al. (2004) J. Physiol. Pharmacol., 55(Suppl. 3) 67-75 (finding similar incidence of CMV in a comparison of 16IPF and 16 normal patients).

Nevertheless, the identification of Herpesviruses in clinical specimenshas spurred the investigation of the use of traditional antiviralreagents to slow or stop the progress of IPF. Administration ofvalacyclovir to two patients with IPF showed mixed results. See Tang etal. (2003) J. Clin. Microbiol. 41; 2633-2640. Administration ofganciclovir to a group of IPF patients with advanced disease also showedmixed results, with 8 patients showing some improvement and 6 patientssuffering further deterioration. See Egan et al. (2011) PulmonaryMedicine 2011. Lastly, a randomized multicenter clinical trial ofinterferon-γ showed no increase in longevity as a result of treatment.See King et al. (2009) Lancet 374(9685):222-228. Accordingly, theseresults do not provide support for the use of traditional antiviralreagents for treatment of IPF.

As previously described in U.S. patent application Ser. No. 13/920,964,filed Jun. 18, 1013, it has been discovered that Herpesvirus saimiri, aherpesvirus that is endemic and nonpathogenic in squirrel monkeys, andwhich was previously unknown to be associated with any human disease,causes or is associated with IPF. Specifically, the inventors discoveredthat 22 out of 22 lung tissue samples from IPF patients showed thepresence of Herpesvirus saimiri DNA, while 25 out of 25 non-IPF sampleshad a complete absence of the virus DNA. This discovery and the factthat herpesviruses are known to cause human disease have led to thesearch for an association between HVS infection and other humandiseases.

There remains a need for effective therapeutic regimens to stopprogression or even reverse the course of diseases such as IPF that areassociated with HVS infection in patients. There also remains a need forearly detection and monitoring of diseases such as IPF that areassociated with HVS infection in patients.

3. SUMMARY

The present disclosure relates to methods of diagnosing orprognosticating a viral disease in a patient comprising a step ofdetecting the presence of a virus-specific element from a virus in aclinical sample from said patient. In various embodiments, thevirus-specific element is selected from a nucleic acid, a protein or apeptide derived from a virus-specific protein.

In various embodiments, the present disclosure relates to methods ofidentifying in vitro a therapeutic agent for the treatment of a viraldisease, comprising the steps of (a) exposing a virus culture to saidagent; (b) measuring the propagation of said virus culture; and (c)comparing said propagation measured in step (b) with the propagation ofa virus culture that has not been exposed to the agent, whereinpropagation measured in step (b) that is lower than propagation of avirus culture that has not been exposed to the agent identifies atherapeutic agent for the treatment of said viral disease.

In still other embodiments, the present disclosure relates to a methodof treating a patient suffering from a viral disease comprisingadministering to the patient an effective amount of an agent thatinhibits replication of a virus, an effective amount of an agent thatdown-regulates expression of a virus-specific protein, an antagonist ofa viral protein or a neutralizing agent that blocks activity of a viralprotein. In certain embodiments, agent is an antagonist, and theantagonist is an antibody to virus-specific IL-17.

In various embodiments, the present disclosure relates to kits fordiagnosing a viral disease in a patient comprising (a) a reagent forcarrying out amplification of a nucleic acid sequence; (b) a primercomprising a sequence complementary to a sequence in one strand of theviral genome; and (c) a primer comprising a sequence identical to asequence in said strand of the viral genome, wherein said primers arecapable of amplifying a nucleic acid of said virus when said nucleicacid is present.

In specific embodiments, the viral disease is idiopathic pulmonaryfibrosis. In other embodiments, the viral disease is alymphoproliferative disease or cancer, such as Castleman's disease inpatients not suffering from AIDS, a thymoma, a lymphoma, or a sarcoma.

Accordingly, in various embodiments, the present disclosure relates tomethods of detecting the presence of viral target sequences in a humanclinical sample comprising the steps of: (a) providing (i) a humanclinical sample suspected of having a viral infection, (ii) a labelednucleic acid probe comprising one or more sequences derived fromHerpesvirus saimiri or a related virus, (b) contacting the clinicalsample with the labeled nucleic acid probe, (c) allowing hybridizationto take place between the labeled nucleic acid probe and the viraltarget sequences in the clinical sample, if present, and (d) detectinghybridization of the nucleic acid probe to the viral target sequences inthe clinical sample. In certain embodiments, the viral target sequencesare from a patient suffering from idiopathic pulmonary fibrosis. Inother embodiments, the viral target sequences are from a patientsuffering from Castleman's disease, a lymphoma, a thymoma or a sarcoma.

In additional embodiments, the present disclosure relates to a method ofdiagnosing Castleman's disease, a lymphoma, a thymoma or a sarcoma in ahuman patient comprising (a) providing (i) a human clinical samplesuspected of having Castleman's disease, a lymphoma, a thymoma or asarcoma, (ii) a labeled nucleic acid probe comprising one or moresequences derived from Herpesvirus saimiri or a related virus, (b)contacting the clinical sample with the labeled probe, (c) allowinghybridization to take place between the labeled nucleic acid probe andthe viral sequences in the clinical sample, if present, and (d)detecting hybridization of the nucleic acid probe to the viral sequencesin the clinical sample, thereby diagnosing the patient as havingCastleman's disease, a lymphoma, a thymoma or a sarcoma.

In still other embodiments, the present disclosure relates to a methodof diagnosing idiopathic pulmonary fibrosis in a human patientcomprising (a) providing (i) a human clinical sample suspected of havingIPF, (ii) a labeled nucleic acid probe comprising one or more sequencesfrom Herpesvirus saimiri or a related virus, (b) contacting the clinicalsample with the labeled nucleic acid probe, (c) allowing hybridizationto take place between the labeled nucleic acid probe and viral sequencesin the clinical sample, if present, and (d) detecting hybridization ofthe nucleic acid probe to the viral sequences in the clinical sample,thereby diagnosing the patient as having idiopathic pulmonary fibrosis.

It should be noted that the indefinite articles “a” and “an” and thedefinite article “the” are used in the present application to mean oneor more unless the context clearly dictates otherwise. Further, the term“or” is used in the present application to mean the disjunctive “or” orthe conjunctive “and.”

All publications mentioned in this specification are herein incorporatedby reference. Any discussion of documents, acts, materials, devices,articles or the like that has been included in this specification issolely for the purpose of providing a context for the presentdisclosure. It is not to be taken as an admission that any or all ofthese matters form part of the prior art or were common generalknowledge in the field relevant to the present disclosure as it existedanywhere before the priority date of this application.

The features and advantages of the disclosure will become furtherapparent from the following detailed description of embodiments thereof.

4. BRIEF DESCRIPTION OF THE FIGURES

FIGS. 1A-1B. Lung tissue samples from an IPF or lung cancer patientstained with Herpesvirus saimiri-specific probes. FIG. 1A provides alung tissue specimen from an IPF patient hybridized with a Herpesvirussaimiri transformation-associated protein (“STP”) specific probe. FIG.1B provides a lung tissue specimen from a lung cancer patient hybridizedwith the STP probe.

FIGS. 2A-2B. Lung tissue sample from an IPF patient stained withHerpesvirus saimiri-specific probes. FIG. 2A provides a lung tissuespecimen from an IPF patient hybridized with a Herpesvirus saimiriSTP-specific probe. FIG. 2B provides a lung tissue specimen from an IPFpatient hybridized with a Herpesvirus saimiri Terminal region (“TER”)probe.

FIGS. 3A-3H. Correlation of IPF histopathology and Herpesvirus saimiridistribution in lung tissue. FIG. 3A provides a correlation of IPFhistopathology and Herpesvirus saimiri distribution in a lung tissuespecimen from an IPF patient stained with hematoxylin and eosin at 25×magnification. FIG. 3B provides the lung tissue sample from FIG. 3A at100× magnification. FIG. 3C provides the tissue specimen of FIG. 3A at400× magnification. FIG. 3D provides a correlation of IPF histopathologyand Herpesvirus saimiri distribution in a lung tissue specimen from anIPF patient stained with blue (virus) and nuclear fast red(counterstain) Herpesvirus saimiri-specific probes at 100×magnification. FIG. 3E shows unremarkable lung tissue adjacent to anarea of IPF. FIG. 3F provides a lung tissue specimen from a patientsuffering from interstitial pneumonitis of known etiology (measlesvirus) stained with Herpesvirus saimiri STP probes. FIG. 3G provides alung tissue specimen from an IPF patient stained with Herpesvirussaimiri STP probes at 400× magnification. FIG. 3H provides a lung tissuespecimen from an IPF patient stained with Herpesvirus saimiri TER probesat 400× magnification.

FIGS. 4A-4B. Nucleotide and protein sequence comparisons of human IL-17and Herpesvirus saimiri IL-17. FIG. 4A provides a comparison of theamino acid sequences of human IL-17 (SEQ ID NO:1) and Herpesvirussaimiri IL-17 (SEQ ID NO:2). FIG. 4B provides a comparison of thenucleotide sequences of the gene encoding human IL-17 (SEQ ID NO:3) andthe gene encoding Herpesvirus saimiri IL-17 (SEQ ID NO:4).

FIGS. 5A-5H. Expression of Herpesvirus saimiri proteins in IPF patientsamples. FIG. 5A provides a lung tissue specimen of regeneratingepithelial cells from an IPF patient stained with a polyclonal antibodyagainst Herpesvirus saimiri cyclin D using a fast red signal andhematoxylin counterstain at 100× magnification. FIG. 5B shows cyclin Dexpression in a normal area of lung tissue sample from an IPF patient at400× magnification. FIG. 5C shows cyclin D expression in an area of lungtissue undergoing active fibrosis at 400× magnification. FIG. 5Dprovides a lung tissue specimen from an IPF patient stained with apolyclonal antibody against Herpesvirus saimiri dihydrofolate reductase(“DHFR”) using a fast red signal and hematoxylin counterstain at 100×magnification. FIG. 5E shows unremarkable lung tissue adjacent to anarea of IPF. FIG. 5F provides a lung tissue specimen from an IPF patientstained with a polyclonal antibody against Herpesvirus saimirithymidylate synthase (“TS”) using a DAB signal and hematoxylincounterstain at 400× magnification. FIG. 5G provides a lung tissuespecimen from a lung cancer patient stained with a polyclonal antibodyagainst human DHFR using a fast red signal and hematoxylin counterstainat 400× magnification. FIG. 5H provides a lung tissue specimen from alung cancer patient stained with a polyclonal antibody against humancyclin D using a fast red signal and hematoxylin counterstain at 400×magnification.

FIGS. 6A-6H. Co-localized expression of Herpesvirus saimiri DNA andproteins. FIG. 6A provides a tissue specimen from an IPF patient thatshows co-localization of nucleic acid signal from Herpesvirus saimiriDNA targets stained with NTB/BCIP and an anti-TS antibody to Herpesvirussaimiri TS stained with DAB. FIG. 6B provides a Nuance conversion ofFIG. 6A showing signal from Herpesvirus saimiri DNA in blue and signalfrom the anti-TS antibody in red, where areas of co-localized expressionare in yellow. FIG. 6C provides a tissue specimen from an IPF patentthat shows co-localization of nucleic acid signal from Herpesvirussaimiri DNA targets stained with NTB/BCIP and an anti-IL-17 antibody toHerpesvirus saimiri IL-17 stained with DAB. FIG. 6D provides a Nuanceconversion of FIG. 6C showing signal from Herpesvirus saimiri DNA inblue and signal from the anti-IL-17 antibody in red, where areas ofco-localization are in yellow. FIG. 6E provides a tissue specimen froman IPF patient that shows co-localization of nucleic acid signal fromHerpesvirus saimiri STP DNA stained with NTB/BCIP and an anti-cyclin Dantibody to Herpesvirus saimiri cyclin D stained with fast red signal.FIG. 6F provides a Nuance conversion of FIG. 6E showing signal fromHerpesvirus saimiri DNA in blue, signal from the anti-cyclin D antibodyin red and where areas of co-localization are in yellow. FIG. 6Gprovides a tissue specimen from an IPF patient that showsco-localization of nucleic acid signal from Herpesvirus saimiri TER DNAstained with NTb/BCIP and an anti-cyclin D antibody to Herpesvirussaimiri cyclin D stained with fast red. FIG. 6H provides a Nuanceconversion of FIG. 6G showing signal from the Herpesvirus saimiri DNA inblue, signal from the anti-cyclin D antibody in red and where areas ofco-localization are yellow.

FIGS. 7A-7I. Herpesvirus saimiri positive B-cells in idiopathicCastleman's disease. FIG. 7A provides a tissue specimen from amediastinal lymph node of a patient with Castleman's disease stainedwith hematoxylin and eosin and a central expanded germinal centersurrounded by typical “onion-skin” layering of hyperplastic B-cells. Theinterfollicular zone is noted as the “T cell zone”. FIG. 7B provides thespecimen of FIG. 7A after in-situ hybridization for HVS DNA using TERprobes with NTB/BCIP (blue) as the chromogen and with a pinkcounterstain. Viral DNA is localized to the “onion-skin” layered areascontaining hyperplastic B-cells. The T-cell zone is negative for theviral DNA. FIG. 7C provides the tissue specimen of FIG. 7A afterimmunohistochemistry for CD20 (B-cells) with DAB (brown) as thechromogen and with a blue counterstain and shows that the expandedgerminal center and surrounding hyperplastic mantle zone consist mostlyof B-cells. FIG. 7D provides the tissue specimen of FIG. 7A afterimmunohistochemistry for viral IL-17 with DAB (brown) as the chromogenand with a blue counterstain and shows that few virus-infected B-cellsin the expanded germinal center express IL-17, which is indicative of alatent infection. FIG. 7E shows the serial section from the mediastinallymph node of FIG. 7A after immunohistochemistry for CD3 (T-cells) withDAB (brown) as the chromogen and with a blue counterstain and shows thatT-cells localize primarily to the interfollicular zone. FIG. 7F providesthe serial section of FIG. 7E probed for the presence of IL-6 with DAB(brown) as the chromogen and with a blue counterstain and shows that thedistribution of CD3+ cells matches the distribution of cells expressingIL-6, indicating that T-cells are producing IL-6. FIG. 7G providesco-expression analyses for IL-6 and CD-3, where fluorescent yellowindicates the cells expressing both proteins. Most cells expressing IL-6are T-cells, whereas the B-cell zone to the left of the IL-6+/CD3+ cellsare negative for both markers. FIG. 7H provides the specimen of FIG. 7Aafter in-situ hybridization for HVS DNA using STP probes, NBT/BCIP(blue) as the chromogen and with a pink counterstain. Viral DNAlocalizes to the “onion-skin” layered areas which contain thehyperplastic B-cells, while the interfollicular zone which consists ofT-cells is negative for viral DNA. FIG. 7I provides the specimen of FIG.7A after in-situ hybridization for HVS RNA using herpesvirus saimiriU-rich noncoding RNA probes, NBT/BCIP (blue) as the chromogen and with apink counterstain showing many lymphocytes positive for HVS RNA in theregion of an expanded mantle zone.

FIGS. 8A-8D. Herpesvirus saimiri positive cells in a thymoma. FIG. 8Aprovides a tissue specimen from a thymoma after in-situ hybridizationwith HVS STP probes using NBT/BCIP (blue/black) as the chromogen andwith a pink counterstain. A number of HVS+ cells are identified by thearrows. FIG. 8B provides a tissue specimen from a different thymoma thanin FIG. 8A after in-situ hybridization with HVS STP probes usingNBT/BCIP (blue/black) as the chromogen and with a pink counterstain. Anumber of HVS+ cells in this second specimen are identified by thearrows. FIG. 8C provides the tissue sample of FIG. 8B afterimmunohistochemistry for viral IL-17 using DAB (brown) and CD20 usingFast Red signal (red) at high magnification. The specimen showsrelatively few IL-17 producing cells and scattered CD20+ cells. FIG. 8Dprovides the tissue sample of FIG. 8B after immunohistochemistry forviral cyclin D1 with DAB (brown) as the chromogen and with a bluecounterstain. The specimen shows relatively few cyclin D1 producingcells.

FIGS. 9A-9B. Herpesvirus saimiri positive cells in sarcomas. FIG. 9Aprovides a tissue specimen from a patient suffering from aretroperitoneal liposarcoma after in-situ hybridization for HVS usingSTP and TER probes using NBT/BCIP (blue/black) as the chromogen and witha pink counterstain. A number of HVS+ cancer cells show signallocalization to the nucleus. FIG. 9B provides a tissue specimen from adifferent patient suffering from a retroperitoneal liposarcoma afterin-situ hybridization for HVS using STP and TER probes using NBT/BCIP(blue/black) as the chromogen and with a pink counterstain. A number ofHVS+ cells are identified by the arrows.

FIGS. 10A-10D. Detection of Herpesvirus saimiri DNA with biotinylatedprobes. FIG. 10A provides a tissue specimen from an IPF patient analyzedfor viral IL-17 using the biotinylated probe described in Example 9 andimmunohistochemistry for cyclin D1 with DAB (brown) as the chromogen andwith a blue counterstain at 400× magnification. FIG. 10B provides aNuance conversion of FIG. 10A where the signal for the DNA is blue andsignal from the anti-cyclin D antibody in green, where areas ofco-localized expression are in yellow. FIG. 10C provides a serialsection from the sample of FIG. 2A analyzed for viral DNA polymeraseusing the biotinylated probe described in Example 9 andimmunohistochemistry for cyclin D1 with DAB (brown) as the chromogen andwith a blue counterstain at 400× magnification. FIG. 10D provides aNuance conversion of FIG. 10A where the signal for the DNA is blue andsignal from the anti-cyclin D antibody in green, where areas ofco-localized expression are in yellow.

5. DETAILED DESCRIPTION

The present invention is based on the inventors' unexpected discoverythat Herpesvirus saimiri, a herpesvirus that is endemic andnonpathogenic in squirrel monkeys, and which was previously unknown tobe associated with any human disease, causes or is associated with IPF.Specifically, the inventors have discovered that 22 out of 22 lungtissue samples from IPF patients showed the presence of Herpesvirussaimiri DNA, while 25 out of 25 non-IPF samples had a complete absenceof the virus DNA. In addition, the present invention is based on theunexpected discovery that Herpesvirus saimiri causes or is associatedwith tumor or other neoplastic initiation in humans, includinglymphoproliferative diseases and cancer, such as Castleman's disease inpatients not suffering from AIDS (“idiopathic Castleman's disease”),thymomas, lymphomas, and sarcomas. Specifically, the present inventorshave discovered that 13 out of 13 tissue samples from patients sufferingfrom idiopathic Castleman's disease were positive for Herpesvirussaimiri nucleic acids, whereas none of the control patients testedpositive for the virus. Furthermore, the present inventors havediscovered that Herpesvirus saimiri nucleic acids were present in 6 outof 12 tissue samples from patients with mediastinal or retroperitoneallymphomas, while no virus was detected in 12 cases of B-cell lymphomas.

Accordingly, the present disclosure relates to methods and compositionsfor diagnosing, prognosticating and/or monitoring disease progression ina patient known or suspected to be suffering from a viral disease. Thepresent disclosure further relates to methods and compositions fordetermining the efficacy of therapy in a patient suffering from a viraldisease. In still other embodiments, the present disclosure relates tokits for diagnosing, prognosticating and/or monitoring diseaseprogression in a patient known or suspected to be suffering from a viraldisease. In some embodiments, the present disclosure relates to methodsand compositions for identifying a therapeutic agent for the treatmentof a viral disease. In various embodiments, the disclosure relates tomethods and compositions for treating a viral disease, and to vaccinecompositions for preventing a viral disease by immunizing a subjectagainst infection by a virus.

5.1. Definitions

As used herein, the term “patient” refers to a human subject sufferingfrom or susceptible to a viral disease or who has been exposed to avirus.

The terms “virus” and “viral” as used herein refer to a disease-causingagent that includes Herpesvirus saimiri, including Herpesvirus saimiristrain A (“HVS A”), Herpesvirus saimiri strain B (“HVS B”) andHerpesvirus saimiri strain C (“HVS C”). The terms “virus” and “viral”further include any related virus, wherein a “related virus” is definedas a virus that has at least 50%, such as at least about 55%, such as atleast about 60%, such as at least about 65%, such as at least about 70%,such as at least about 75%, such as at least about 80%, such as at leastabout 85%, such as at least about 90%, such as at least about 95%, orsuch as at least about 99% or more sequence homology of the entire viralgenome independently to the entire viral genome of HVS A, or the entirevial genome of HVS B or the entire viral genome of HVS C. For theavoidance of doubt, the genome sequence homology referred to herein isnot related to a specific gene or gene segment, but to the homology ofthe entire genome of a virus to the entire genome of HVS A, or theentire genome of HVS B, or the entire genome of HVS C. The term“Herpesvirus saimiri” when not identified by a specific strain will beunderstood to include HVS A, HVS B and HVS C.

In the context of the present invention, the term “novel virus” refersto a herpesvirus that is not Herpesvirus saimiri but that is related toit. Specifically, a “novel virus” is a herpes gammavirus having lessthan 95% homology of the L region with the L region of Herpesvirussaimiri and having 50% or more homology of the L region with the Lregion of Herpesvirus saimiri. A virus having 95% or more homology inthe L region is Herpesvirus saimiri. Furthermore, the gammavirus that isdescribed as having the closest homology with Herpesvirus saimiri isHerpesvirus ateles (Ehlers et al. (2008) J Virol 82; 3509-3516; Lacosteet al. (2010) Inf Genet Evol 10; 1-13) which has about 35% homology withthe L region of Herpesvirus saimi (Fleckenstein et al. (1978) J Vir 25;361-373).

The term “viral disease” as used herein refers to a clinicalmanifestation in a human that is caused by or associated with infectionof a virus that includes Herpesvirus saimiri, including HVS A, HVS B andHVS C. The term “viral disease” further includes a clinicalmanifestation in a human that is caused by or associated with a relatedvirus. A “viral disease” includes, but is not limited to, idiopathicpulmonary fibrosis (IPF), lymphoproliferative diseases and cancer. Incertain embodiments, the lymphoproliferative diseases and cancerinclude, but are not limited to, idiopathic Castleman's disease,thymomas, lymphomas, and sarcomas. The term “idiopathic Castleman'sdisease” refers to Castleman's disease that has heretofor had no knowncause, and excludes Castleman's disease in patients with HIV infection.Over 90% of Castleman's disease is idiopathic.

As used herein, the terms “unrelated virus” and “unrelated viruses”refer to any virus that has less than 50% homology in the entire viralgenome to the entire viral genome of HVS A, or the entire viral genomeof HVS B or the entire viral genome of HVS C.

As used herein, the term “virus-specific element” includes any substancederived directly or indirectly from Herpesvirus saimiri or a relatedvirus, including but not limited to, a viral nucleic acid, a viralprotein, a peptide derived from a viral protein, a direct or indirectmetabolite of a viral protein and/or a patient antibody to avirus-specific element, including but not limited to, envelope proteinsof the virus. In some embodiments, a virus-specific element is a virallycoded protein involved in viral propagation, viral replication, viralparticle assembly or viral latency. In some particular embodiments, theviral protein is a viral analog of a human protein, such as a viralanalog of IL-17. In other embodiments, the peptide is derived from aprotein that is a viral analog of a human protein (e.g., a peptide froma viral analog of IL-17). In some embodiments, the virus-specificelement is an enzyme, such as TS or DHFR. In other embodiments, theviral analog of a human protein is selected from IL-17, TS, DHFR, andcyclin D. In other embodiments, the viral protein is a viral envelopeprotein or viral capsid protein. In some embodiments, the virus-specificelement is the whole virus itself. In still other embodiments, thevirus-specific element is a cell that is infected by the virus andthereby expresses a viral-specific element in the cell or on the cellsurface.

As used herein, the term “viral metabolite” includes a product of anenzyme of Herpesvirus saimiri or a related virus such as a polymerase,kinase, synthase, protease, reductase, primase, glycosylase,phosphatase, helicase, terminase, transferase, and the like. In someembodiments, the enzyme is unique to the virus. In other embodiments,the enzyme is a viral analog of a host (human) protein.

As used herein, the term “viral property” refers to viral propagation,viral replication, and a virus-specific enzyme, protein or metabolitethat are important in the disease-causing process. As described herein,detection of the presence of Herpesvirus saimiri or a related virusand/or association of Herpesvirus saimiri or a related virus with aviral disease means detecting a viral property. In addition, methods oftreating or preventing (e.g., by vaccination) a viral disease is by wayof manipulation of a viral property.

As used herein, the term “patient antibody” to a virus-specific elementincludes any antibody produced by a patient that specifically binds to avirus-specific element of Herpesvirus saimiri or a related virus. Apatient antibody includes, but is not limited to, a cell-surface boundantibody and an antibody that is not bound to a cell surface. Thepatient antibody can have any isotype, including IgA, IgD, IgE, IgG andIgM.

As used herein, the terms “antibody” or “antibodies” when referring toan antibody that is not a patient antibody as described above includes,but is not limited to, a human antibody, in which the entire sequence isa human sequence, a humanized antibody, which is an antibody fromnon-human species whose protein sequences have been modified to increasetheir similarity to antibody variants produced naturally in humans, anda chimeric antibody, which have certain domains from one organism (e.g.,mouse) and other domains from a second organism (e.g., human) to yield,e.g., a partially mouse, partially human antibody. The antibody caninclude, but is not limited to, an antibody or antibody fragment such asFab, Fab′, F(ab)₂, an Fv fragment, a diabody, a tribody, a linearantibody, a single chain antibody molecule (e.g. scFv) or amulti-specific antibody formed by fusions of antibody fragments. Invarious embodiments, the antibody is polyclonal, monoclonal,multispecific, primatized, or an antibody fragment. In particularembodiments, the antibody is a monoclonal antibody. See, e.g., Riechmannet al. (1988) Nature 332(6162):332-323; Queen et al. (1989) Proc NatlAcad Sci USA. 86 (24):10029-33; Nishimura et al. (1987) Cancer Res.47:999-1005.

As used herein, the term “clinical sample” refers to a sample from apatient and includes, but is not limited to, whole blood, serum, lungtissue, lavage (e.g., bronchiolar lavage), and formalin fixed paraffinembedded tissue.

The terms “hybrid,” “hybridize,” “hybridization” and the like refer tothe non-covalent interaction between fully complementary or partiallycomplementary nucleic acid sequences. In various embodiments, theseterms may be used interchangeably herein, for example, a step ofdetecting “hybridization” of a nucleic acid probe to a target sequencehas the same meaning as detecting the “hybrid” of a nucleic acid probeand a target sequence.

The term “nucleotide analogue” is a variant of a natural nucleotide,such as DNA or RNA nucleotides, by introduction of one or moremodifications. In various embodiments, these modifications whenincorporated into a nucleic acid will have a functional effect on theproperties of the nucleic acid, for example, conferring higher or lowerbinding affinity for a target sequence, conferring detectability byinclusion of a label and/or conferring the property of degeneratebinding to target nucleic acids.

The phrases “treatment of,” “treating”, and the like include theamelioration or cessation of a condition or a symptom thereof. In oneembodiment, treating includes inhibiting, for example, decreasing theoverall frequency of episodes of a condition or a symptom thereof.

The phrases “prevention of,” “preventing”, and the like include theavoidance of the onset of a condition or a symptom thereof.

The term “therapeutic agent” for the treatment of a viral disease, asused herein, refers to an agent identified by the methods described inSection 6.4, the agents described in Section 6.5, known agents for thetreatment of viral diseases and combinations thereof.

5.2. Methods for Diagnosing or Prognosticating a Viral Disease,Monitoring Disease Progression and Monitoring the Efficacy of Therapy

In certain embodiments, the present disclosure relates to methods fordiagnosing a viral disease in a patient, which comprises detecting thepresence of a virus-specific element in the patient. In a particularembodiment, the present disclosure relates to methods for diagnosing IPFin a patient, which comprises detecting the presence of a Herpesvirussaimiri-specific element or a related virus-specific element in thepatient. In other embodiments, the present disclosure relates to methodsfor prognosticating a viral disease in a patient by detecting thepresence of a virus-specific element in the patient. In a particularembodiment, the present disclosure relates to methods forprognosticating IPF in a patient by detecting the presence ofHerpesvirus saimiri-specific element or a related virus-specific elementin the patient. In some embodiments, a viral disease is diagnosed orprognosticated in an asymptomatic patient. In other embodiments, a viraldisease is diagnosed in a patient suffering from one or more symptoms.In still other embodiments, a viral disease is diagnosed orprognosticated in a patient with one or more potential risk factors fora viral disease.

It will be understood by the skilled artisan that one or morevirus-specific elements and/or antibodies to a virus-specific elementcan be measured in the methods disclosed herein.

In particular embodiments, the viral disease is IPF. In certainembodiments, IPF is diagnosed in a patient who is suffering frominterstitial lung disease. In yet other embodiments, IPF is diagnosed ina patient who evidences a usual interstitial pneumonia pattern onhigh-resolution computed tomography (HRCT). In still other embodiments,IPF is diagnosed in a patient with one or more potential risk factorsfor IPF, such as cigarette smoking, environmental exposure (e.g., tosquirrel monkeys, birds, chemicals used in hair dressing or farming,stone cutting/polishing, and exposure to livestock and to vegetable dustand/or animal dust), chronic viral infection, and abnormalgastroesophageal reflux. In some embodiments, the methods andcompositions can be used to screen healthy individuals with one or morerisk factors. In yet another embodiment, the methods can be used toscreen healthy individuals with no risk factors.

In other embodiments, the viral disease is selected fromlymphoproliferative diseases and cancer. In certain embodiments, thelymphoproliferative diseases and cancer include, but are not limited to,idiopathic Castleman's disease, thymomas, lymphomas, and sarcomas. Invarious embodiments, the viral disease is retroperitoneal or mediastinallymphocytic proliferation. In some embodiments, the viral disease isretroperitoneal or mediastinal sarcoma. In certain embodiments, theviral disease is gastrointestinal stromal sarcoma. In other embodiments,the viral disease is retroperitoneal liposarcoma.

In various embodiments, the present disclosure also relates to methodsof monitoring the progression of a viral disease in a patient, whichcomprises measuring a first level of a virus-specific element and/or apatient antibody to a virus-specific element in a first clinical samplefrom the patient, measuring a second level of a virus-specific elementand/or a patient antibody to a virus-specific element in a secondclinical sample from the patient and comparing the first level ofvirus-specific element and/or antibody with the second level ofvirus-specific element and/or antibody, wherein a first level ofvirus-specific element and/or antibody that is lower than a second levelof virus-specific element and/or antibody is indicative of diseaseprogression. In certain embodiments, the viral disease to be monitoredis IPF and the virus-specific element is from Herpesvirus saimiri or arelated virus and/or the antibody is specific for a Herpesvirussaimiri-specific element or a related virus-specific element. In otherembodiments, the viral disease to be monitored is selected from alymphoproliferative disease and cancer. In certain embodiments, thelymphoproliferative disease and cancer include, but are not limited to,idiopathic Castleman's disease, thymomas, lymphomas, and sarcomas, andthe virus-specific element is from Herpesvirus saimiri or a relatedvirus and/or the antibody is specific for a Herpesvirus saimiri-specificelement or a related virus-specific element. In various embodiments, thesecond clinical sample is collected from the patient at least about 1day, at least about 1 week, at least about 2 weeks, at least about 3weeks, at least about 1 month, at least about 3 months, at least about 6months, at least about 9 months, at least about 12 months or more afterthe first clinical sample is collected.

In still other embodiments, the disclosure relates to methods ofmonitoring the efficacy of a therapy for the treatment of a viraldisease, which comprises measuring a first level of a virus-specificelement and/or patient antibody to a virus-specific element in a firstclinical sample from an untreated patient, measuring a second level of avirus-specific element and/or patient antibody to a virus-specificelement in a second clinical sample from the patient after treatment andcomparing the first level of virus-specific element and/or antibody andthe second level of virus-specific element and/or antibody, wherein afirst level of a virus-specific element and/or antibody that is greaterthan the second level of the virus-specific element and/or antibody isindicative of the efficacy of the therapy. In certain embodiments, theviral disease is IPF and the virus-specific element is derived fromHerpesvirus saimiri or a related virus and/or the antibody is specificfor a Herpesvirus saimiri-specific element or a related virus-specificelement. In other embodiments, the viral disease is selected from alymphoproliferative disease and cancer. In certain embodiments, thelymphoproliferative diseases and cancer include, but are not limited to,idiopathic Castleman's disease, thymomas, lymphomas, and sarcomas, andthe virus-specific element is derived from Herpesvirus saimiri or arelated virus and/or the antibody is specific for a Herpesvirussaimiri-specific element or a related virus-specific element. In variousembodiments, the second clinical sample is collected from the patient atleast about 1 day, at least about 1 week, at least about 2 weeks, atleast about 3 weeks, at least about 1 month, at least about 3 months, atleast about 6 months, at least about 9 months, at least about 12 monthsor more after the therapy is administered to the patient. The skilledartisan will understand that an “untreated patient” may refer to apatient who has not had any treatment for the viral disease or to apatient who was previously treated with a therapy for the viral diseasethat is different from the therapy being monitored in the methodsdisclosed herein.

The discovery that the presence of Herpesvirus saimiri is highlycorrelated with IPF and other diseases such as lymphoproliferativediseases and cancer in patients allows for the development of methodsand compositions for diagnosing or prognosticating a viral disease, suchas IPF, lymphoproliferative diseases and cancer, in a patient and/ormethods for monitoring the progression of a viral disease and/or methodsfor monitoring the efficacy of therapy in a patient suffering from aviral disease in lieu of elaborate histochemical analyses orhigh-resolution computed tomography. In certain embodiments, the diseasethat is diagnosed or prognosticated is IPF. In other embodiments, thedisease that is diagnosed or prognosticated is selected from alymphoproliferative disease (e.g., Castleman's disease), a thymoma, alymphoma, and a sarcoma. In some embodiments, the virus-specific elementdetected in a clinical sample is a viral nucleic acid and the detectionmethods are carried out using one or more nucleic acid probes thatspecifically bind to a viral nucleic acid. In certain embodiments, theviral nucleic acid is RNA. In the context of the present disclosure, RNAincludes both spliced and unspliced RNA molecules transcribed from thegenome, such as mRNA and small U-RNAs that do not code for proteins. Inother embodiments, the viral nucleic acid is DNA. In some embodiments,the nucleic acid is purified from the clinical sample before detection.In other embodiments, the nucleic acid is not purified from the clinicalsample before detection.

In certain embodiments, the detection is carried out by specificallyhybridizing a nucleic acid from the clinical sample with a nucleic acidprobe. In other embodiments, the detection is carried out by firstmaking a copy of a nucleic acid from the clinical sample and thenspecifically hybridizing the nucleic acid copy with a nucleic acidprobe. In some embodiments, the nucleic acid probe comprises a sequencefrom viral DNA. In other embodiments, the nucleic acid probe comprises asequence that is complementary to a nucleic acid sequence from viralDNA. In certain embodiments, the viral DNA is from Herpesvirus saimiri.In still other embodiments, the nucleic acid probe comprises a sequencethat is complementary to a nucleic acid sequence from viral RNA. In yetadditional embodiments, the nucleic acid probe comprises a sequence thatis complementary to a nucleic acid sequence from viral mRNA. In certainembodiments, the viral RNA is from Herpesvirus saimiri or a relatedvirus. As used herein, a nucleic acid from a clinical sample thatspecifically hybridizes to a nucleic acid probe means that the nucleicacid and the probe have a sufficient degree of complementarity to avoidnon-specific binding of the nucleic acid under the conditions of theassay.

In various embodiments, nucleic acid probes that specifically bind to aviral nucleic acid sequence are used for directly detecting targetnucleic acids by fluorescent in-situ hybridization (FISH) as describedin Example 1. In other embodiments, detection of viral nucleic acids iscarried out by isolation of nucleic acids from a clinical sample,binding to a matrix and detection with a labeled probe. Examples of suchmethods can include dot blot, slot blot, Northern blot, Southern blotand a sandwich assay. In other specific embodiments, labeled nucleicacid probes that specifically bind to viral nucleic acid sequences areused in conjunction with flow cytometry to identify the presence of thevirus in cells. See Coquillard et al. (2011) Gynecologic Oncol. 120;89-93. In still other embodiments, nucleic acids from a clinical sampleare labeled and hybridized with probes that specifically bind to viralnucleic acids. In various embodiments, the probes are immobilized on asolid support, e.g., in a microarray, beads or a reverse dot blot. Incertain particular embodiments, e.g., when the detection is performed insitu, detection is carried out fluorescently or enzymatically. See,e.g., Langer-Safer et al. (1982) Proc. Natl. Acad. Sci. U.S.A. 79 (14):4381-85. In other embodiments of the present invention, no labelednucleic acids are used and detection of viral DNA is carried out by wayof a Gardella gel. See Gardella et al. (1984) J. Virol. 50:248-254.

Nucleic acids can be labeled by any method known in the art. In someembodiments, the label is a radioactive label. In other embodiments, thelabel is a non-radioactive label. In certain embodiments, thenon-radioactive label is selected from a fluorescent label, achemiluminscent label, a hapten label, a chromogenic label, and anenergy transfer pair. Such fluorescent labels include, but are notlimited to, xanthene dyes, anthracene dyes, cyanine dyes, porphyrindyes, rhodamine dyes, coumarin dyes and dyes disclosed in any of U.S.Pat. Nos. 8,247,179, 7,569,695, 8,153,802, 8,389,729, and U.S. PatentPublication No. 2012/0040430, each of which is incorporated herein byreference in its entirety. In certain embodiments, the fluorescent labelis covalently attached to one or more nucleotides on the sugar, base,phosphate or a combination thereof. In other embodiments, thefluorescent label is not covalently attached to the nucleic acid, butbinds to double-stranded nucleic acids, for example, an intercalator. Invarious embodiments, the non-radioactive label is a chemiluminescentlabel. In other embodiments, the label is a chromogenic label, e.g., acompound such as the 1,2-dioxetane reagents disclosed in U.S. Pat. No.8,247,179 that comprise two groups attached to different sites of acyclic ring where after catalysis by an appropriate enzyme, the reagentundergoes an intramolecular reaction, thereby leading to signalgeneration. In still other embodiments, the label is an energy transferpair. The skilled artisan will understand that energy transfer can bebetween labeled primers, a labeled primer and one or more labelednucleotides, labeled nucleotides, a labeled primer and a labelednucleotide or nucleotides, a labeled probe and a labeled nucleotide ornucleotides, and the like. See U.S. Pat. No. 8,247,179 for discussion ofenergy transfer protocols. In particular embodiments, the first energytransfer element and the second energy transfer element areindependently selected from fluorescein, fluorescein isothiocyanate(FITC), 6-carboxyfluorescein (6-FAM), naphthofluorescein, rhodamine,rhodamine 6G, rhodamine X, rhodol, sulforhodamine 101,tetramethylrhodamine (TAMRA), tetramethylrhodamineisothiocyanate(TRITC), 4,7-dichlororhodamine, eosin, eosinisothiocyanate (EITC),dansyl, hydroxycoumarin, methoxycoumarin or p-(Dimethyl aminophenylazo)benzoic acid (DABCYL), cyanine dyes, or derivatives of any of theforegoing. In various embodiments, the label is a hapten, a highlyimmunogenic compound that is detected by binding of labeled anti-haptenantibodies. Such haptens include, but are not limited to, digoxigenin,DNP (dinitrophenol), biotin, and fluorescein (which is also afluorescent dye). In various embodiments, the nucleic acid label is acompound that can be detected by binding to a labeled binding partnerother than an antibody, such as biotin, avidin or streptavidin. Invarious embodiments, the nucleic acid is bound to an enzymatic label—anenzyme whose presence can be detected by the addition of a substratethat the enzyme converts to a detectable product. In certainembodiments, a label is attached directly to the nucleic acid. In otherembodiments, the label is attached via a linker arm. Various linker armsthat are useful for attaching a label to a nucleic acid can be found,for example, in U.S. Pat. No. 8,247,179.

In certain embodiments, the methods described herein further include astep of amplifying the signal for increasing the sensitivity ofdetection. In various embodiments, methods for signal amplificationinclude, but are not limited to, detection with bDNA probes, detectionwith antibodies against DNA/RNA hybrids, use of gold nanoparticles(Verigene), use of the Invader system and rolling circle amplification(RCA). See, e.g., Terry et al. (2001) J. Med. Virol. 65; 155-162;Storhoff et al. (2004) Nature Biotechnology 22; 883-887; Hall et al.(2000) Proc. Nat. Acad. Sci. USA 97; 8272-8277; Lizardi et al., (1998)Nat. Genet. 19; 225-232.

In other embodiments, the methods described herein further include astep of amplifying nucleic acids before detection. In certainembodiments, nucleic acids are amplified by PCR or RT-PCR. In certainembodiments, the amplifying step comprises global amplification of anyand all sequences as is typically done when using whole-genomeamplification (WGA) or expression arrays. A common method used foramplification of RNA from expression arrays is the Eberwine method(Eberwine et al. (1992) Proc. Nat. Acad. Sci. (USA) 89:3010-14) andexemplary methods for WGA are degenerate oligonucletotide primer PCR(DOP-PCR) as described in Telenius et al. (1992) Genomics 13:718-725,and multiple displacement amplification (MDA) as described in Dean etal. (2002) Proc. Nat'l Acad. Sci. (USA) 99:5261-5266. In otherembodiments, amplification may utilize target-specific primers or areverse transcription step to allow specific amplification of viralnucleic acids. Analysis of amplified products can be performed byend-point PCR using, e.g., a sandwich assay, dot blot, Southern blot,Northern blot, microarray or Mass Spectrometry (including electrosprayionization mass spectrometry of PCR products) or real-time PCR.Microarray formats include probes spotted or synthesized onto solidmatrices or bead based formats, including but not limited to, slidearrays (Agilent Technologies), in situ synthesized microarrays(Affymetrix), bead arrays (Illumina) and coded beads detected by flowcytometry using XTag technology (Luminex). Real-time detection methodsfor PCR include, but are not limited to, detection with SYBR green,Taqman assays, Molecular Beacons, Sunrise primers, Scorpion primers,Light-up probes and the AmpiProbe (Enzo Life Sciences) system describedin U.S. Pat. No. 8,247,179. See also, Hofstadler et al. (2005) Int J.Mass Spec. 242; 23-41; Wilhelm et al. (2003) ChemBioChem 4; 1120-1128;Arya et al. (2005) Expert Rev. Molec. Diagn. 5; 209-219.

In various embodiments, nucleic acid amplification can be accomplishedby isothermal methods. Such isothermal amplification methods that can beused in the methods described herein include, but are not limited to, aSelf-Sustained Sequence Reaction (3SR), a Nucleic acid BasedTranscription Assay (NASBA), a Transcription Mediated Amplification(TMA), a Strand Displacement Amplification (SDA), a Helicase-DependentAmplification (HDA), a Loop-Mediated isothermal amplification (LAMP),stem-loop amplification, signal mediated amplification of RNA technology(SMART), isothermal multiple displacement amplification (IMDA), a singleprimer isothermal amplification (SPIA), and a circularhelicase-dependent amplification (cHDA). See, e.g., Notomi et al. (2000)Nucl. Acids Res. 28:e63; U.S. Pat. No. 6,743,605; Gill et al., (2008)Nucleosides, Nucleotides, and Nucleic Acids 27:224-243. The skilledartisan will understand that most signal generation systems typicallyused for PCR can be applied to end-point and real-time detection methodsusing isothermal amplification systems.

In various embodiments, viral nucleic acid targets for detection in themethods described herein include any nucleic acid sequence that ispresent in the genome of Herpesvirus saimiri or a related virus, but notthe genome of unrelated viruses that infect humans, or in the humangenome. Accordingly, probes for detection of virus can be designed tospecifically bind to such unique sequences. Sequences that may also beincluded for this purpose include fusion products derived from splicingof mRNA species of Herpesvirus saimiri or a related virus where thejunctions generate new sequences that are only partially present in thegenome. In particular embodiments, viral nucleic acid targets fordetection of a virus in the methods described herein preferably includea nucleic acid target that is conserved between virus strains, such asnucleic acid targets that code for proteins involved in virusreplication or viral assembly. Accordingly, in some embodiments, thenucleic acid target is selected from major single-stranded DNA bindingprotein (mDNA-BP) gene sequences, DNA polymerase gene sequences, DNApackaging terminase gene sequences, helicase-primase complex genesequences, uracil DNA glycosylase gene sequences, deoxyuridinetriphosphatase (dUTPase) gene sequences, DNA polymerase processivityfactor gene sequences, and capsid assembly and DNA maturation proteingene sequences. In other embodiments, the nucleic acid target isselected from TER gene sequences, STP gene sequences, repeat sequencesof the virus, and sequences of genes that have been adopted by the virusfrom mammalian systems, such as, IL-17 gene sequences, Cyclin D genesequences, dihydrofolate reductase (DHFR) gene sequences, andthymidylate synthase gene sequences. In still other embodiments, thenucleic acid target is selected from glycoprotein B gene sequences, Saggene sequences, CD59 gene sequences, Bcl2 gene sequences, capsid proteingene sequences, envelope protein gene sequences, ribonucleotidereductase gene sequences, tegument protein gene sequences, FLICEinteracting protein (FLIP) gene sequences, IL-8 receptor gene sequences,glycoprotein M gene sequences, and FGARAT gene sequences. In additionalembodiments, the nucleic acid target is selected from thymidine kinasegene sequences, phosphotransferase gene sequences, and tyrosine kinasegene sequences. In various embodiments, viral nucleic acid targets fordetection of Herpesvirus saimiri or a related virus in the methodsdescribed herein include any gene in the viral genome. In otherembodiments of the present disclosure, amplification is carried out withprimers that amplify a variety of different viral sequences andidentification of the particular type of herpesvirus is carried out withone or more species-specific probes or by restriction enzyme digestion.Examples of such techniques are described by VanDevanter et al. (1996)J. Clin. Micro. 34:1666-1671; Chmielewicz et al. (2001) Virus Research75:87-94.

It will be evident to the skilled artisan that unique sequences of avirus can be identified by comparing the degree of complementaritybetween a reference sequence from the virus genome with human and/orunrelated virus sequences. In determining the degree of“complementarily” between the virus and unrelated virus or human nucleicacids, the degree of “complementarity” (also, “homology”) is expressedas the percentage identity between the sequence of the virus sequence(or region thereof) and the reverse complement of the sequence of theregion of the human or unrelated virus nucleic acid that best alignstherewith. The percentage is calculated by counting the number ofaligned bases that are identical as between the 2 sequences, dividing bythe total number of contiguous monomers in the reference sequence, andmultiplying by 100. Polynucleotide alignments, percentage sequenceidentity, and degree of complementarity may be determined for purposesof the invention using the ClustalW algorithm using standard settings:Method: EMBOSS::water (local): Gap Open=10.0, Gap extend=0.5, usingBlosum 62 (protein), or DNAfull for nucleotide/nucleobase sequences.Also useful for this purpose are various forms of BLAST searches.

In various embodiments in which the method comprises detecting more thanone virus nucleic acid, the detection of the plurality of nucleic acidsmay be detected concurrently or simultaneously in the same assayreaction. In some embodiments, the detection of the plurality of nucleicacids is carried out concurrently or simultaneously in separatereactions. In some embodiments, detection is carried out at differenttimes, such as in serial assay reactions.

In some embodiments, the methods of detecting a nucleic acid ofHerpesvirus saimiri or a related virus described herein employ one ormore modified oligonucleotides. In certain embodiments, theoligonucleotides comprise one or more affinity-enhancing nucleotides.Modified oligonucleotides for use in the methods described hereininclude probes and primers for reverse transcription and/oramplification. In some embodiments, the incorporation ofaffinity-enhancing nucleotides increases the binding affinity andspecificity of an oligonucleotide for its target nucleic acid ascompared to oligonucleotides that contain only deoxyribonucleotides, andallows for the use of shorter oligonucleotides or for shorter regions ofcomplementarity between the oligonucleotide and the viral nucleic acid.

In some embodiments, affinity-modulating nucleotides include nucleotidescomprising one or more base modifications, sugar modifications and/orbackbone modifications.

In some embodiments, modified bases for use in affinity-modulatingnucleotides include 5-methylcytosine, isocytosine, pseudoisocytosine,5-bromouracil, 5-propynyluracil, 6-aminopurine, 2-aminopurine, inosine,diaminopurine, 2-chloro-6-aminopurine, xanthine and hypoxanthine.

In other embodiments, affinity-modulating modifications includenucleotides having modified sugars such as 2′-substituted sugars, suchas 2′-O-alkyl-ribose sugars, 2′-amino-deoxyribose sugars,2′-fluoro-deoxyribose sugars, 2′-fluoro-arabinose sugars, and2′-O-methoxyethyl-ribose (2′MOE) sugars. In some embodiments, modifiedsugars are arabinose sugars, or d-arabino-hexitol sugars.

In still other embodiments, affinity-modulating modifications includebackbone modifications such as peptide nucleic acids (e.g., an oligomerincluding nucleobases linked together by an amino acid backbone). Otherbackbone modifications include phosphorothioate linkages, phosphodiestermodified nucleic acids, combinations of phosphodiester andphosphorothioate linkages, methylphosphonates, alkylphosphonates,phosphate esters, alkylphosphonothioates, phosphoramidates, carbamates,carbonates, phosphate triesters, acetamidates, carboxymethyl esters,methylphosphorothioate, phosphorodithioate, p-ethoxy, and combinationsthereof.

In some embodiments, the oligomer includes at least oneaffinity-enhancing nucleotide that has a modified base, at least onenucleotide (which may be the same nucleotide) that has a modified sugar,and at least one internucleotide linkage that is non-naturallyoccurring.

In some embodiments, the affinity-enhancing oligonucleotide contains alocked nucleic acid (“LNA”) sugar, which is a bicyclic sugar. In someembodiments, an oligonucleotide for use in the methods described hereincomprises one or more nucleotides having an LNA sugar. In someembodiments, the oligonucleotide contains one or more regions consistingof nucleotides with LNA sugars. In other embodiments, theoligonucleotide contains nucleotides with LNA sugars interspersed withdeoxyribonucleotides. See, e.g., Frieden, M. et al. (2008) Curr. Pharm.Des. 14(11):1138-1142.

In certain embodiments, the oligomer includes at least one universalbase, i.e., a base that can base pair with more than one complementarybase, were first used in oligonucleotides to maintain stablehybridization with target nucleic acids that had ambiguity in theidentity of their nucleotide sequence. A well-known example of this isthe substitution of inosine in PCR primes (Liu and Nichols, (1994)Biotechniques 16; 24-26). Inosine has the property of being able to basepair efficiently with either G, A, T or C in a complementary strand(Kawase et al., 1986, Nucl. Acids Res. 19; 7727-7736). The meltingtemperature is less than a normal base pairing but still higher than amismatch. When used as a template, inosine is recognized as if it waseffectively G and a C is preferentially incorporated into thecomplementary copy. Other analogs of nucleotides that can act asuniversal bases have also been described. For instance,5-nitroindolenine and 3-nitopyrrole analogues have also been describedas universal bases (Loakes and Brown, 1994, Nucl. Acids Res. 22;4039-4043, Nichols et al., 1994, Nature 369; 492-493 both of which areincorporated by reference). The use of these and other universal basesare reviewed by Loakes (2001) in Nucl. Acids Res. 29; 2437-2447(incorporated by reference). The ability of universal bases to addstability without adding to the complexity of primers has been describedby Ball et al., (1998, Nucl. Acids Res. 26; 5225-5227, incorporated byreference) where the addition of 5-nitroindolenine residues at the 5′end, improved the specificity and signal intensity of octamer primersused for cycle sequencing. Thus, these and other universal bases may allfind use in the present invention.

In another embodiment of the present invention, a protein is detected.In some embodiments, the protein is a virus-specific protein. In certainembodiments, the virus-specific protein is an analog of a human protein.In particular embodiments, the protein to be detected is selected fromIL-17, thymidylate synthase, dihydrofolate reductase, cyclin D, STP,Sag, CD59, Bcl2, FGARAT, FLIP, a peptide derived from any of theforegoing and combinations thereof. In other particular embodiments, theprotein to be detected is a viral envelope protein or a capsid proteinsuch as VP23, glycoprotein M, and FGARAT, a peptide derived from any ofthe foregoing, and combinations thereof. Accordingly, in variousembodiments, the presence of virus-specific proteins is detected byimmunological methods. Immunological reagents that bind to viralantigens (e.g., proteins or peptides) can be generated and selected byany method taught in the art. Such reagents include, but are not limitedto, antibodies and antibody fragments such as Fab, Fab′, F(ab)₂ and Fvfragments, diabodies, tribodies, linear antibodies, single chainantibody molecules (e.g. scFv) and multi-specific antibodies formed byfusions of antibody fragments. See, e.g., Holliger et al. (2005) NatureBiotechnology 23:1126-1136.

Methods of selecting appropriate antigen binding reagents, e.g.,antibodies that recognize viral antigens, but that do not cross-reactwith unrelated viral antigens or human antigens, can be accomplished byany method known in the art. Accordingly, in some embodiments, anantibody is developed by immunizing a mammalian host, e.g., a goat orrabbit, with one or more viral proteins or peptides and, after asuitable time period (and possible booster shots), identifying cellsthat secrete an appropriate antibody. In other embodiments, anartificial system for antigen binding reagent selection, such as librarydisplays, can be used. In these embodiments, pre-made antibody librariesare screened for reactivity to a specific antigen. In some embodiments,negative selection can be used to eliminate antigen binding reagentsthat have affinity for inappropriate targets. See, e.g., Hoogenboom(2005) Nature Biotechnology 23:1105-1116. The skilled artisan willunderstand that an appropriate antigen binding agent for detection ofvirus-specific proteins will react with the protein of Herpesvirussaimiri or a related virus, but not with the human protein or with aprotein from an unrelated virus.

In some embodiments, the antibody is a primary antibody for directdetection of the viral antigen. In other embodiments, detection iscarried out by a secondary antibody that binds to the primary antibodyin an immunoassay. Secondary antibodies can be any antibody that bindsto a constant region of the primary antibody, including but not limitedto, an anti-mouse antibody, an anti-rabbit antibody, an anti-goatantibody and the like. Antibodies can be labeled by any method known inthe art. In certain embodiments, a label, e.g., a fluorescent dye, achemiluminescent compound, a radioactive label, a hapten label, achromogenic label, an energy transfer pair, or a compound that can bedetected by binding to a labeled binding partner, such as biotin, avidinor streptavidin, is covalently attached, either directly or through alinker arm (e.g., maleimide), to either the primary or secondaryantibody. In various embodiments, a label is non-covalently bound to aprimary antibody or a secondary antibody. In still other embodiments,the primary antibody or the secondary antibody is covalently ornon-covalently bound to an enzyme whose presence can be detected by theaddition of a substrate that the enzyme converts to a detectableproduct. Non-limiting examples of such enzymes include, but are notlimited to, alkaline phosphatase, horseradish peroxidase, andluciferase.

Antibodies for detection and/or quantification of virus-specificelements can be used in any assay known in the art for detection ofproteins of interest, including enzyme-linked immune sorbent assays(“ELISA”), such as indirect ELISA, sandwich ELISA, competitive ELISA andmultiple and portable ELISA, histological detection, protein chip arraysand bead assays. A variety of different assay formats for detectingproteins and various means of signal generation are discussed in Pei etal. (2012) Analytica Chimica Acta 758:1-18.

As discussed above, the antibodies referred to herein can be any type ofantibody, including, but not limited to polyclonal, monoclonal, chimerichuman, humanized, multispecific, primatized, a single chain or anantibody fragment such as Fab, ScFv, Fab′, F(ab′)2, Fv, Fv(ab)2 orcombinations thereof. See, e.g., Hollinger & Hudson (2005) NatureBiotechnol. 23(9):1126-1136 for a review of useful engineered antibodyfragments and single antibody domains. Antibodies for use in the presentinvention can be developed and isolated by any method known in the art.In certain embodiments, antibodies can be identified by screening ofrecombinant antibody libraries using, for example, platforms such asphage display, ribosome and mRNA display, microbial cell (such as yeastcell) display, and directed evolution platforms such as retroviraldisplay, display based on protein-DNA linkage, microbead display by invitro compartmentalization, in vivo-based growth selection based on theprotein fragment complementation assay (PCA) or other systems andsingle-molecule sorting. Selection procedures include identification andselection of antibodies that bind to specific antigens, selection ofantibodies with improved binding affinity or kinetics toward a targetantigen, and screening of target-binding properties of particularantibodies. In certain embodiments, the antibody is optimized by, forexample, affinity maturation, humanization, selection for biophysicalproperties (e.g., thermostability, resistance to proteases, etc.). SeeHoogenboom et al. (2005) Nature Biotechnol 23(9):1105-1116 for a reviewof selection and screening methods and antibody optimization strategies.In particular embodiments, antibodies to structural and/ornon-structural proteins from Herpesvirus saimiri, a related virus or anovel virus can be obtained or identified by any method known in theart. In various embodiments, anti-viral antibodies can be obtained byimmunizing mice with purified virions and creating hybridomas forscreening to identify hybridomas secreting specific antibodies to viralantigens and binding can be characterized by known methods, such asWestern blotting. See, e.g., Dahlberg et al. (1985) J Virol53(1):279-286 for exemplary methods of producing and characterizingmonoclonal antibodies to Herpesvirus saimiri proteins. In still otherembodiments, antibodies can be identified and/or characterized usingrecombinant viral proteins. See, e.g., Randall et al. (1984) J Virol52(3):872-883. Recombinant viral proteins, such as viral IL-17 can beobtained by known methods or are available from commercial sources.

In certain embodiments, the virus-specific protein is an enzyme and isdetected using an enzyme activity assay. Enzyme assays can be performedby any method known in the art, including, but not limited to,spectrophotometric assays (including colorimetric assays such as an MTTassay), fluorometric assays, calorimetric assays, chemiluminescentassays, light scattering assays, microscale thermophoresis assays,radiometric assays and chromatographic assays. See, e.g., Bergmeyer(1974). Methods of Enzymatic Analysis 4. New York: Academic Press. pp.2066-72; Passonneau et al. (1993). Enzymatic Analysis. A PracticalGuide. Totowa N.J.: Humana Press. pp. 85-110; Todd et al. (2001). Anal.Biochem. 296 (2): 179-87; Churchwella et al. (2005) J Chromatog B 825(2):134-143. Specific assays for Herpesvirus enzymes can be found, forexample, in Nicholas et al. (1998) J Natl Cancer Inst Monogr. 23:79-88.In some embodiments, the enzyme is selected from thymidine kinase,phosphotransferase, tyrosine kinase, uracil DNA glycosylase,deoxyuridine triphosphatase, TS and DHFR.

In some embodiments where the viral protein is a viral analog of a humanprotein, a virus can be detected by detecting aberrant expression of theviral protein. As used herein “aberrant expression” refers to expressionof a protein in a cell, tissue, organ or body fluid of a patient thatdoes not normally produce the protein in a healthy individual(inappropriate expression) or expression of higher levels of a proteinin a cell, tissue, organ or body fluid of a patient than are detected inthe same type of cell, tissue, organ or body fluid of a healthyindividual (differential expression). In various embodiments, aberrantexpression is detected using an antibody that specifically binds to theviral protein, but not to the human protein. In other embodiments,aberrant expression is detected using an antibody that binds to both thehuman protein and the viral analog of the human protein. Accordingly, incertain embodiments where the antibody binds to both the human proteinand the viral analog, the detected aberrant expression is at least about10%, such as at least about 15%, such as at least about 20%, such as atleast about 25%, such as at least about 30%, such as at least about 35%,such as at least about 40%, such as at least about 45%, such as at leastabout 50% or greater than expression of the human protein in a healthyindividual. It will be understood by the skilled artisan, that in someembodiments, a peptide of a viral protein can also be detected in thedisclosed methods. In various embodiments, aberrant expression isdetected in an immunological assay, such as ELISA. In situ detection mayalso be carried out for detection in cells where undetectable levels areseen only in the absence of disease. In still other embodiments in whichthe protein is an enzyme, aberrant expression is detected by affinitypurification followed by an enzyme assay.

In certain embodiments where the viral protein is an enzyme that is aviral analog of a human enzyme, a virus can be detected by detectingaberrant expression of a metabolite of the enzyme. Accordingly, in someembodiments, the metabolite is detected by inappropriate expression in acell, tissue, organ or body fluid of a patient that does not normallyproduce the metabolite in a healthy individual. In other embodiments,the metabolite is detected by differential expression, such asexpression of higher levels of the metabolite in a cell, tissue, organor body fluid of a patient than are detected in the same type of cell,tissue, organ or body fluid of a healthy individual. Accordingly, incertain embodiments, the detected aberrant expression of the metaboliteis at least about 10%, such as at least about 15%, such as at leastabout 20%, such as at least about 25%, such as at least about 30%, suchas at least about 35%, such as at least about 40%, such as at leastabout 45%, such as at least about 50% or greater than expression of themetabolite in a healthy individual. Methods of detecting and/orquantifying enzyme metabolites are known in the art. Such methodsinclude, but are not limited to, gas chromatography, high performanceliquid chromatography, capillary electrophoresis, mass spectrometry,surface-based mass analysis such as MALDI and secondary ion massspectrometry (SIMS), desorption electrospray ionization (DESI) andnuclear magnetic resonance (NMR). Schauer et al. (2005) FEBS Lett.579(6):1332-7; Gika et al. (2007) J. Proteome Res. 6(8):3291-303; Sogaet al. (2003) J. Proteome Res. 2(5):488-494; Northen et al. (2007)Nature 449(7165):1033-6; Woo et al. (2008) Nature Protocols 3(8):1341-9; Griffin (2003) Curr Opin Chem Biol 7(5):648-54; Beckonert etal. (2007) Nat Protoc 2(11):2692-703.

In various embodiments, detection of a virus-specific protein, peptideor metabolite comprises a step of separating and/or purifying theprotein, peptide or metabolite to be measured. In particularembodiments, the method includes a step of quantifying the protein,peptide or metabolite. Separation and/or purification of proteins,peptides and/or metabolites can be accomplished by any method known inthe art, including, but not limited to, liquid chromatography techniques(e.g., HPLC, affinity chromatography, size-exclusion chromatography,ion-exchange chromatography and combinations thereof), electrophoresis(e.g., capillary electrophoresis, gel electrophoresis and the like) andimmunological methods (e.g., antibody capture). Methods of quantifying aprotein, peptide or metabolite can be accomplished by any method knownin the art, including, but not limited to, quantitative massspectrometry, two-dimensional gel electrophoresis, immunoassay (e.g.,ELISA) and the like.

In various embodiments, the viral protein is a cytokine. In someembodiments, the cytokine is a viral analog of a human cytokine. Incertain of these embodiments, detection of a viral analog of a humancytokine can be performed using an antibody that binds to the viralcytokine but not to the human cytokine. In other embodiments, detectioncan be performed using an antibody that binds to both the viral cytokineand the human cytokine. In still other embodiments, the viral cytokineis detected in a cell proliferation assay, such as a T-cellproliferation assay. T-cell proliferation can be measured by any methodknown in the art, such as by cell counting using flow cytometry,[³H]-thymidine uptake and the like. Various methods for measuring T-cellproliferation can be found for example in U.S. patent application Ser.No. 13/871,730 and references cited therein.

In various embodiments, a patient antibody to a virus-specific elementis detected. In some embodiments, the virus-specific element is part ofthe viral envelope. In other embodiments, the virus-specific element ispart of the viral capsid. In other embodiments, the virus-specificelement is not part of the viral envelope or the viral capsid, but canbe released from the interior of the virus, for example, by dissociationof the viral particles. In other embodiments, the virus-specific elementis released by during lysis of a host cell. In some embodiments, thepresence of a patient antibody to the virus is indicative of latency ofviral infection. In other embodiments, the presence of a patientantibody to the virus is indicative of exposure to the virus in theabsence of established infection. Patient antibodies to a virus-specificelement can be detected and/or quantified by any method known in theart, including, but not limited to, Western blotting, ELISA, amicroparticle enzyme immunosorbent assay, a magnetic immunoassay, and anELISPOT assay. Other methods for detection of patient antibodies can befound in Corchero et al. (2001) Clinical and Diagnostic LaboratoryImmunol. 8(5):913-921.

In other embodiments, the virus or a cell infected by the virus isdetected. In certain embodiments, the virus is detected using anantibody that specifically binds to an envelope protein or a capsidprotein of the virus. In some embodiments, the virus is detected in animmunoassay, such as an ELISA assay. In other embodiments, the virus isdetected by flow cytometry. In some embodiments, the cells are derivedfrom tissue. In some embodiments, serum or whole blood is analyzed. Inother embodiments, peripheral blood cells are examined for the presenceof virus. In these embodiments, peripheral blood is obtained from apatient and mononuclear cells are separated, e.g., by centrifugationonto Ficoll-Hypaque. The cell layer at the interface is removed, washedin phosphate-buffered saline without Ca2+ and Mg2+, and fixed with 90%methanol, and intracellular viral antigens are detected, e.g., byindirect immunofluorescence with antibodies to viral antigens as theprimary antibody and a labeled secondary antibody and/or by flowcytometry.

5.3. Kits for Diagnosing or Prognosticating a Viral Disease, MonitoringDisease Progression and Monitoring the Efficacy of Therapy

In some embodiments, the present disclosure relates to kits fordiagnosing or prognosticating a viral disease in a patient. In otherembodiments, the present disclosure relates to kits for monitoringdisease progression and/or monitoring the efficacy of therapy in apatient. In various embodiments, the kits are for detection ofHerpesvirus saimiri or a related virus in a clinical sample from apatient. In certain embodiments, the kit comprises one or more reagentsfor detecting a virus-specific nucleic acid. In other embodiments, thekit comprises one or more reagents for detecting a virus-specificprotein, peptide or metabolite in a clinical sample. In still otherembodiments, the kit comprises one or more reagents for detecting apatient antibody to a virus-specific element. In certain embodiments,the kits are for detection of Herpesvirus saimiri or a Herpesvirussaimiri-specific element. In other embodiments, the kits are fordetection of a related virus, or a related virus-specific element.

In certain embodiments where the kit is for detection of virus-specificnucleic acids, the kit includes oligonucleotide probes that specificallybind to a virus-specific nucleic acid. In some embodiments, theoligonucleotide probes comprise one or more affinity-modulatingnucleotides. Such affinity-enhancing nucleotides include nucleotidescomprising one or more base modifications, sugar modifications and/orbackbone modifications. In some embodiments, modified bases for use inaffinity-enhancing nucleotides include 5-methylcytosine, isocytosine,pseudoisocytosine, 5-bromouracil, 5-propynyluracil, 6-aminopurine,2-aminopurine, inosine, diaminopurine, 2-chloro-6-aminopurine, xanthineand hypoxanthine. In other embodiments, affinity-enhancing modificationsinclude nucleotides having modified sugars such as 2′-substitutedsugars, such as 2′-O-alkyl-ribose sugars, 2′-amino-deoxyribose sugars,2′-fluoro-deoxyribose sugars, 2′-fluoro-arabinose sugars, and2′-O-methoxyethyl-ribose (2′MOE) sugars. In some embodiments, modifiedsugars are arabinose sugars, or d-arabino-hexitol sugars.

In still other embodiments, affinity-modulating modifications includebackbone modifications such as peptide nucleic acids (e.g., an oligomerincluding nucleobases linked together by an amino acid backbone). Otherbackbone modifications include phosphorothioate linkages, phosphodiestermodified nucleic acids, combinations of phosphodiester andphosphorothioate linkages, methylphosphonates, alkylphosphonates,phosphate esters, alkylphosphonothioates, phosphoramidates, carbamates,carbonates, phosphate triesters, acetamidates, carboxymethyl esters,methylphosphorothioate, phosphorodithioate, p-ethoxy, and combinationsthereof. In some embodiments, the affinity-enhancing oligonucleotidecontains a locked nucleic acid (“LNA”) sugar, which is a bicyclic sugar.In some embodiments, an oligonucleotide for use in the methods describedherein comprises one or more nucleotides having a modified backbone,e.g., an LNA or a peptide nucleic acid. In other embodiments, theoligonucleotide contains one or more regions consisting of nucleotideswith modified backbones. In various embodiments, all of the nucleotideshave a modified backbone. In other embodiments, the oligonucleotidecontains nucleotides having a modified backbone interspersed withdeoxyribonucleotides. See, e.g., Frieden, M. et al. (2008) Curr. Pharm.Des. 14(11):1138-1142.

In some embodiments, the probes include at least one affinity-modulatingnucleotide that has a modified base, at least one nucleotide (which maybe the same nucleotide) that has a modified sugar, and at least oneinternucleotide linkage that is non-naturally occurring.

In some embodiments, the virus-specific probes for inclusion in the kitare lyophilized and can be reconstituted in an appropriate buffer. Inother embodiments, the virus-specific probes are bound to a solidsupport, e.g., an addressable array or magnetic beads.

In some embodiments, where the kit is for detection of viral nucleicacids, the kit may further include one or more reagents for amplifying anucleic acid of interest. Such one or more reagents may include, but isnot limited to, virus-specific primers and a polymerase.

In other embodiments, the kits are for detection of a virus-specificprotein, peptide or metabolite. In some embodiments, the kits are fordetection and quantification of a virus-specific protein, peptide ormetabolite, for example, to detect inappropriate expression ordifferential expression of a virus-specific protein, a peptide derivedfrom a virus-specific protein or a metabolite. In these latterembodiments, the kit can include one or more reagents for quantificationof a protein, peptide or metabolite, such as a Bradford reagent orantibody that specifically binds to a virus-specific protein, peptide ormetabolite. In various embodiments, the virus-specific protein is fromHerpesvirus saimiri or a related virus and the antibody specificallybinds to a viral protein selected from IL-17, TS, DHFR, cyclin D, Sag,CD59, Bcl2, FGARAT, FLIP, a viral envelope protein, a viral capsidprotein, a protein involved in viral replication, or a peptide derivedfrom any of these proteins. In various embodiments, the virus-specificelement is a virus-specific metabolite. In these embodiments, themetabolite is a product of a virus-specific enzyme, such as thymidylatesynthase, dihydrofolate reductase, thymidine kinase, phosphotransferase,tyrosine kinase, uracil DNA glycosylase, or deoxyuridine triphosphatase.

In some embodiments, the kit includes an immunological reagent thatspecifically binds to a virus-specific protein, peptide or metabolite,for example, an antibody or antibody fragment such as Fab, Fab′, F(ab)₂,an Fv fragment, a diabody, a tribody, a linear antibody, a single chainantibody molecule (e.g. scFv) or a multi-specific antibody formed byfusions of antibody fragments. See, e.g., Holliger et al. (2005) NatureBiotechnology 23:1126-1136. In certain embodiments, the kit includes aprimary antibody that specifically binds to a virus-specific protein,peptide or metabolite derived therefrom. In other embodiments, the kitincludes a primary antibody that specifically binds to a virus-specificprotein, peptide or metabolite derived therefrom and a secondaryantibody that binds to the primary antibody. In various embodiments, theprimary antibody and/or the secondary antibody is labeled. In otherembodiments, the kit includes one or more reagents for labeling theprimary antibody and/or the secondary antibody. In some embodiments, thelabel is selected from a fluorescent dye, a chemiluminescent compound, aradioactive label, a hapten label, a chromogenic label, an energytransfer pair, a compound that can be detected by binding to a labeledbinding partner, such as biotin, avidin or streptavidin, and an enzymewhose presence can be detected by the addition of a substrate that theenzyme converts to a detectable product. In some embodiments, the labelis covalently attached to the antibody. In other embodiments, the labelis non-covalently attached to the antibody. In still other embodiments,the label is attached directly to the antibody. In some embodiments, thelinker comprises a labeled nucleic acid. See, e.g., U.S. Pat. No.7,514,551; U.S. Patent Publication No. 2010/0273145 and Zheng et al.(2007) Bioconjugate Chemistry 18:1668-1672. In yet other embodiments,the label is attached indirectly to the antibody through a linker arm.In some embodiments, the kit further includes standards forquantification of virus-specific proteins, peptides and/or metabolites.

In still other embodiments, the kits are for detection of humanantibodies to Herpesvirus saimiri or a related virus. In someembodiments, the kit comprises an immunological reagent thatspecifically binds to a patient antibody raised against epitopes ofHerpesvirus saimiri or a related virus. In other embodiments, the kitincludes a primary antibody that specifically binds to a patientantibody raised against a virus, or peptide derived therefrom, and asecondary antibody that binds to the primary antibody. In variousembodiments, the primary antibody and/or the secondary antibody islabeled. In other embodiments, the kit includes one or more reagents forlabeling the primary antibody and/or the secondary antibody. In someembodiments, the label is selected from a fluorescent dye, achemiluminescent compound, a radioactive label, a hapten label, achromogenic label, an energy transfer pair, a compound that can bedetected by binding to a labeled binding partner, such as biotin, avidinor streptavidin, and an enzyme whose presence can be detected by theaddition of a substrate that the enzyme converts to a detectableproduct. In some embodiments, the label is covalently attached to theantibody. In other embodiments, the label is non-covalently attached tothe antibody. In still other embodiments, the label is attached directlyto the antibody. In yet other embodiments, the label is attachedindirectly to the antibody through a linker arm. In some embodiments,the kit further includes standards for quantification of humananti-viral antibodies.

In various embodiments, the kits are for detection of Herpesvirussaimiri, a related virus and/or a host cell that is infected by thevirus. In certain embodiments, the kit comprises an antibody thatspecifically binds to a virus envelope protein or a virus capsidprotein. In other embodiments, the kit comprises an antibody thatspecifically binds to a viral marker on the surface of an infected hostcell, e.g., a blood cell. In certain embodiments, for example, when thevirus or infected cell is identified by immunoassay, the kit can furtherinclude a secondary antibody that binds to the primary antibody thatbinds to a cell-surface marker, a virus envelope protein or a viruscapsid protein. In still other embodiments, the kit comprises one ormore reagents, e.g., antibodies to host cell-surface and/orvirus-envelope or capsid markers that are fluorescently labeled for usein flow cytometry, and in particular, fluorescence-activated cellsorting (FACs) based on the cell- or virus-envelope or capsid markers.In various embodiments, the kit may further include one or more antibodylabeling reagents.

In other embodiments, the various kits described herein include one ormore of (i) a cell line for culturing a virus; (ii) a cell growthmedium; and/or (iii) a buffer. In certain embodiments, the cell line isa permissive cell line selected from owl monkey kidney cells,co-cultured epithelial cells and peripheral blood cells from naturallyinfected squirrel monkeys. In other embodiments, the cell line is apermissive cell line such as Raji B-cells, HFF fibroblasts and PANC-1epithelial cells. In still other embodiments, the cell line is asemi-permissive cell line, e.g., T-cells such as Jurkat cells, CCRF-CEMand Molt 3 cells, B-cells such as BALL-1 and Daudi cells, epithelialcells such as 5673 or myeloid/erythroid cell lines including K562 andHEL 92.1.7 cells. See Simmer et al. (1991) J Gen. Vir. 72:1953-58.

5.4. Methods for Identifying a Therapeutic Agent for Treatment of aViral Disease

In certain embodiments, the present disclosure relates to a method ofidentifying a therapeutic agent for the treatment of a viral disease,which comprises the steps of (i) exposing a virus culture to an agent;(ii) measuring the replication or propagation of said virus culture; and(iii) comparing said replication or propagation measured in step (ii)with a the replication or propagation of a virus culture that has notbeen exposed to the agent, wherein replication or propagation measuredin step (ii) that is lower than replication or propagation of the virusculture that has not been exposed to the agent identifies a therapeuticagent for the treatment of the viral disease. In certain specificembodiments, the virus culture is a Herpesvirus saimiri culture. Inother specific embodiments, the virus culture is a related virusculture. In some embodiments, the viral disease is IPF. In otherembodiments, the viral disease is a lymphoproliferative disease orcancer.

In various embodiments, in vitro assays are carried out in humanT-lymphocytes. See Kaschka-Dierich et al. (1982) J Virol 44:295-310.

In certain embodiments, in vitro assays to measure the effect of aputative therapeutic agent on virus infectivity and/or replicationcomprise culturing a virus in a cell line that is permissive for viralinfection. In some embodiments, permissive cell lines that can be usedin the described methods include, but are not limited to, owl monkeykidney cells, and a co-culture of permissive epithelial cells withperipheral blood cells from naturally infected squirrel monkeys. Othercell lines that are useful for this purpose include permissive celllines such as Raji B-cells, HFF fibroblasts and PANC-1 epithelial cells.In still other embodiments, the cell line is a semi-permissive cellline, e.g., T-cells such as Jurkat cells, CCRF-CEM and Molt 3 cells,B-cells such as BALL-1 and Daudi cells, epithelial cells such as 5673 ormyeloid/erythroid cell lines including K562 and HEL 92.1.7 cells. SeeSimmer et al. (1991) J Gen. Vir. 72:1953-58.

In some embodiments, viral replication is measured by counting thenumber of virus particles or the number of infected host cells. Viruscounting techniques include plaque assays, determination of the 50%Tissue Culture Infective Dose, a fluorescence focus assay (FFA),transmission electron microscopy and flow cytometry (such asfluorescence activated cell sorting using fluorescent labeled bindingagents for virus surface antigens). See, e.g, Kaufmann et al. (2002)Methods in Microbiology Vol. 32: Immunology of Infection (AcademicPress); Martin (1978). The Biochemistry of Viruses (Cambridge UniversityPress); Flint et al. (2009) Principles of Virology. ASM Press;Malenovska (2013) J. Virological Methods, doi:10.1016/j.jviromet.2013.04.008; Stoffel et al. (2005) AmericanBiotechnology Laboratory 37 (22): 24-25.

In various embodiments, virus replication is measured by measuring anamount of viral nucleic acid. In some embodiments, the nucleic acid isviral DNA. In particular embodiments, the nucleic acid is Herpesvirussaimiri DNA. In other embodiments, the nucleic acid is viral mRNA. Inparticular embodiments, the nucleic acid is Herpesvirus saimiri mRNA. Invarious embodiments, the step of measuring viral replication is precededby a step of amplifying viral nucleic acids. Exemplary methods fornucleic acid amplification and quantification are set forth in Section6.2, supra.

In other embodiments, viral replication is measured by measuring anamount of viral protein and/or functional activity of a viral protein,e.g., by measuring an amount of a metabolite of the viral protein. Insome embodiments, the assay quantifies the amount of total protein ofthe virus. In other embodiments, the assay quantifies the amount of aspecific viral protein in the sample. In other embodiments, the assayquantifies the amount of functional activity of the viral protein. Insome embodiments, the viral protein is involved in metabolism, and afunctional assay can be carried out by measuring a metabolite producedby enzymatic activity. Examples of such viral proteins include thymidinekinase, phosphotransferase, tyrosine kinase, uracil DNA glycosylase,deoxyuridine triphosphatase, TS and DHFR. In other embodiments, theviral protein is involved in signal secretion, and a functional assaycan be carried out by measuring a reporter gene that is influenced bycytokine/cytokine receptor binding. Examples of such viral proteinsinclude IL-6 and IL-17. In various embodiments, the virus is Herpesvirussaimiri or a related virus and the viral protein that is measured isselected from IL-17, TS, cyclin D, Sag, CD59, Bcl2, FGARAT, FLIP, aviral envelope protein, a viral capsid protein, a protein involved inviral replication, and combinations thereof. In other embodiments, themetabolite is a product of a Herpesvirus saimiri or a related virusthymidine kinase, phosphotransferase, tyrosine kinase, uracil DNAglycosylase, deoxyuridine triphosphatase, TS or DHFR. In someembodiments, protein and/or metabolite detection and quantification isperformed using an assay selected from a bicinchoninic acid assay, asingle radial immunodiffusion assay, mass spectrometry, LabMap assaysand ELISA. See, e.g., Smith et al. (1985) Anal. Biochem. 150 (1): 76-85;Rodda et al. (1981) Journal of Clinical Microbiology 14 (5): 479-482;Kemeny et al. (1988) ELISA and Other Solid Phase Immunoassays:Theoretical and Practical Aspects (John Wiley and Sons); Kuby et al.(2007) Kuby Immunology 6th edition (W.H. Freeman and Company); Dunbar etal. (2003) J Microb Methods 53:245-252. In still other embodiments,viral quantification is accomplished by measuring both viral nucleicacids and viral proteins, for example, by flow cytometry. See Stoffel etal. (2005) American Biotechnology Laboratory 37 (22): 24-25.

The skilled artisan will understand that the methods described hereincan be used for de novo screening of therapeutic agents to determinetheir effects on a virus, or for screening of known drugs, e.g., knownanti-viral agents, cytokine antagonists and the like. Screening can befrom a library of agents. Screening can further be of modified versionsof known drugs, e.g., known anti-viral agents or of combinations ofknown drugs. The skilled artisan will understand that the screeningmethods described herein are applicable to therapeutic agents and/orknown drugs and/or modified versions of known drugs or therapeuticagents alone or in combination. Screening can also include virtualmethods, such as structure-based drug design based on, e.g., thethree-dimensional structure of a virus essential protein such as a DNApolymerase, followed by in vitro testing using the methods describedherein.

5.5. Methods and Compositions for Treating a Viral Disease

The present inventors' unexpected discovery that the presence ofHerpesvirus saimiri is strongly correlated with IPF, and certainlymphoproliferative diseases and cancers, in humans allows for newtreatment approaches for these and other viral diseases. Anti-viralagents for use in the present invention include (i) agents that inhibitpropagation of the virus; (ii) agents that neutralize a component of thevirus; and (iii) agents that inhibit an enzyme of the virus.

Accordingly, in some embodiments, the present disclosure relates tomethods and compositions for inhibiting propagation of Herpesvirussaimiri or a related virus. In certain embodiments, the compositionscomprise an effective amount of a therapeutic agent identified by themethods described in Section 6.4. In various embodiments, thecompositions include one or more therapeutic agents that are knownanti-viral agents, e.g., acyclovir, vidarabine, idoxuridine, brivudine,cytarabine, foscarnet, docosanol, formivirsen, tromantidine, imiquimod,podophyllotoxin, cidofovir, interferon alpha-2b, peginterferon alpha-2a,ribavirin, moroxydine, valacyclovir, trifluridine, andbromovinyldeoxyuridine.

In some embodiments, the agent is an agent that inhibits replication ofthe virus, such as a nucleotide analog that is incorporated into DNA bythe viral DNA polymerase and results in early chain termination. Inother embodiments, the agent binds to and blocks one or more viralpolymerases. In still other embodiments, the agent is directed to viralproteins responsible for viral DNA maturation (cleavage/packaging). Inother embodiments, the agent inhibits episomal persistence of the viralgenome. See Collins et al. (2002) J. Gen. Virol. 83:2269-78.

In other embodiments, the agent down-regulates expression ofvirus-specific proteins. In various embodiments, the virus-specificprotein is selected from viral IL-17, viral IL-10, and thelatency-associated nuclear antigen (LANA). Gene expression can bedown-regulated by any method known in the art, including, but notlimited to, by administering antisense DNA or antisense mRNA, by RNAinterference (RNAi) and by the use of ribozymes to cleave RNAtranscripts.

In other embodiments, the present disclosure relates to methods andcompositions for neutralizing a component of Herpesvirus saimiri or arelated virus. Accordingly, in some embodiments, the neutralizing agentis an antagonist of a viral protein, such as an agent that blocks one ormore interactions of a viral protein with other viral proteins or withhost proteins. In other embodiments, the neutralizing agent blocksactivity of a specific viral protein. In certain embodiments, when theviral protein is a human homolog, the antagonist inhibits ordown-regulates the viral analog without significantly impacting thehuman protein.

In certain embodiments, the neutralizing agent is an antibody. Invarious embodiments, the antibody is a monoclonal antibody. In otherembodiments, the antibody is a polyclonal antibody. In variousembodiments, the antibody is a human antibody. In still otherembodiments, the antibody is a humanized antibody. In particularembodiments, the antagonist is an antibody to virus-specific IL-17. Insome embodiments, the antibody is specific for variants ofvirus-specific IL-17. In specific embodiments, the antibody is specificfor virus-specific IL-17A. In some embodiments, the neutralizing agentis an antibody to an IL-17 receptor (IL17R). In various embodiments, theIL17R antibody is specific for IL17RA. In other embodiments, the IL17Rantibody is specific for IL17RB.

In yet other embodiments, the IL17R is specific for IL17RC. Inadditional embodiments, the antibody is specific for more than one ofIL17RA, IL17RB and IL17RC. In some embodiments, the neutralizing agentis IL-10 or an agonist of IL-10, such as isoproterenol, IT 9302 andcombinations thereof. In other embodiments, the neutralizing agent is aninhibitor of IL-17 expression. In additional embodiments, theneutralizing agent is an inhibitor of expression of one or more IL-17receptors.

In still other embodiments, the neutralizing agent is an antagonist ofTGF-β. In certain embodiments, the antagonist is an antibody to TGF-β.In various embodiments, the antibody is a monoclonal antibody. In otherembodiments, the antibody is a polyclonal antibody. In still otherembodiments, the antibody is a human antibody. In further embodiments,the antibody is humanized. In some embodiments, the neutralizing agentis an antibody to a TGF-β receptor. In certain embodiments, theneutralizing agent is an inhibitor of TGF-β expression. In otherembodiments, the neutralizing agent is an inhibitor of TGF-β receptorexpression.

In various embodiments, the present disclosure relates to methods andcompositions for treating a viral disease in a patient by administeringan effective amount of a neutralizing agent that is an antagonist ofIL-23. In certain embodiments, the neutralizing agent is an antibody toIL-23. In various embodiments, the antibody is a monoclonal antibody. Inother embodiments, the antibody is a polyclonal antibody. In still otherembodiments, the antibody is a human antibody. In further embodiments,the antibody is humanized. In some embodiments, the neutralizing agentis an antibody to an IL-23 receptor. In additional embodiments, theneutralizing agent is an inhibitor of IL-23 expression. In otherembodiments, the neutralizing agent is an inhibitor of IL-23 receptorexpression.

In certain embodiments, the present disclosure relates to methods andcompositions for treating a viral disease in a patient by administeringan effective amount of a neutralizing agent that is an antagonist ofIL-1β. In certain embodiments, the neutralizing agent is an antibody toIL-1β. In various embodiments, the antibody is a monoclonal antibody. Inother embodiments, the antibody is a polyclonal antibody. In still otherembodiments, the antibody is a human antibody. In further embodiments,the antibody is humanized. In some embodiments, the neutralizing agentis Canakinumab. In other embodiments, the neutralizing agent is aninhibitor of IL-1β expression. In yet other embodiments, neutralizingagent is an inhibitor of IL-1β receptor expression.

In various embodiments, the present disclosure relates to methods andcompositions for treating a viral disease in a patient by administeringan effective amount of a neutralizing agent that is a solubleextra-cellular domain of a receptor of a viral protein, e.g., a viralcytokine. Accordingly, in some embodiments, the composition comprises asoluble IL-17R extra-cellular domain, such as a soluble IL17RA, IL17RBor IL17RC extra-cellular domains. In other embodiments, the compositioncomprises a soluble IL-R8 receptor extra-cellular domain. Without beingbound by any particular theory, a soluble extra-cellular domain of acytokine receptor competes with membrane-bound cytokine receptors onhuman cells for binding to the cytokine, thereby neutralizing thedeleterious effects of viral cytokine production in the patient.

In various embodiments, the present disclosure relates to methods andcompositions for treating a viral disease in a patient by administeringan effective amount of an agent that inhibits virus entry into hostcells. Accordingly, in some embodiments, the inhibitor is a smallmolecule, a peptide or a peptide mimetic of a host cell receptor thatbinds to a viral surface protein or glycoprotein and blocks binding ofthe virus to the host cell receptor. In other embodiments, the agent isa soluble extra-cellular domain of a host cell receptor. In still otherembodiments, the inhibitor is a small molecule, a peptide or a peptidemimetic of a viral protein or glycoprotein that binds to a host cellreceptor and blocks binding of the virus to the host cell receptor. Invarious embodiments, the agent is a soluble extra-cellular domain of aviral surface protein or glycoprotein. In still other embodiments, theagent is an antibody that binds to either a viral protein orglycoprotein or the host receptor to inhibit virus entry into the hostcells. In various embodiments, the agent blocks entry of the virus intothe cell.

In various embodiments, the present disclosure relates to methods andcompositions for inhibiting an enzyme of Herpesvirus saimiri or arelated virus. Accordingly, in some embodiments, the enzyme is selectedthymidine kinase, phosphotransferase, tyrosine kinase, uracil DNAglycosylase, deoxyuridine triphosphatase, TS and DHFR. In certainembodiments, the viral inhibitor is a reversible inhibitor. In otherembodiments, the viral inhibitor is an irreversible inhibitor. Invarious embodiments, the viral enzyme inhibitor is a competitiveinhibitor and binds to the same site as the natural substrate. In otherembodiments, the viral enzyme inhibitor is an uncompetitive inhibitorand binds only to the enzyme/substrate complex. In still otherembodiments, the viral enzyme inhibitor is a mixed inhibition inhibitorwhere binding of the inhibitor affects the binding of the substrate, andvice versa. In yet other embodiments, the viral enzyme inhibitor is anon-competitive inhibitor that binds to the enzyme and reduces itsactivity but does not affect the binding of substrate.

In particular embodiments, the competitive inhibitor increases K_(m). Insome embodiments, the competitive inhibitor increases K_(m) by at leastabout 5%, such as at least about 10%, such as at least about 15%, suchas at least about 20%, such as at least about 25%, such as at leastabout 30%, such as at least about 35%, such as at least about 40%, suchas at least about 45%, such as at least about 50%, such as at leastabout 55%, such as at least about 60%, such as at least about 65%, suchas at least about 70%, such as at least about 75%, such as at leastabout 80%, such as at least about 85%, such as at least about 90%, suchas at least about 95%, such as at least about 99% or more as compared tothe K_(m) of the enzyme in the absence of the inhibitor.

In other particular embodiments, the non-competitive inhibitor decreasesV_(max). In various embodiments, the noncompetitive inhibitor decreasesV_(max) by at least about 5%, such as at least about 10%, such as atleast about 15%, such as at least about 20%, such as at least about 25%,such as at least about 30%, such as at least about 35%, such as at leastabout 40%, such as at least about 45%, such as at least about 50%, suchas at least about 55%, such as at least about 60%, such as at leastabout 65%, such as at least about 70%, such as at least about 75%, suchas at least about 80%, such as at least about 85%, such as at leastabout 90%, such as at least about 95%, such as at least about 99% ormore as compared to the V_(max) of the enzyme in the absence of theinhibitor.

In still other embodiments, the mixed inhibition inhibitor increasesK_(m) and decreases V_(max). In some embodiments, the mixed inhibitioninhibitor increases K_(m) by at least about 5%, such as at least about10%, such as at least about 15%, such as at least about 20%, such as atleast about 25%, such as at least about 30%, such as at least about 35%,such as at least about 40%, such as at least about 45%, such as at leastabout 50%, such as at least about 55%, such as at least about 60%, suchas at least about 65%, such as at least about 70%, such as at leastabout 75%, such as at least about 80%, such as at least about 85%, suchas at least about 90%, such as at least about 95%, such as at leastabout 99% or more as compared to the K_(m) of the enzyme in the absenceof the inhibitor. In various embodiments, the mixed inhibition inhibitordecreases V_(max) by at least about 5%, such as at least about 10%, suchas at least about 15%, such as at least about 20%, such as at leastabout 25%, such as at least about 30%, such as at least about 35%, suchas at least about 40%, such as at least about 45%, such as at leastabout 50%, such as at least about 55%, such as at least about 60%, suchas at least about 65%, such as at least about 70%, such as at leastabout 75%, such as at least about 80%, such as at least about 85%, suchas at least about 90%, such as at least about 95%, such as at leastabout 99% or more as compared to the V_(max) of the enzyme in theabsence of the inhibitor. It will be understood that a mixed inhibitioninhibitor, which interferes with substrate binding and catalysis in theenzyme-substrate complex, can have any combination of K_(m) increase andV_(max) decrease, e.g., K_(m) is increased by 20% and V_(max) isdecreased by 50% or K_(m) is increased by 10% and V_(max) is decreasedby 40%, etc.

In other embodiments, the inhibitor is an irreversible enzyme inhibitor.In various embodiments, the irreversible enzyme inhibitor covalentlymodifies an enzyme target. Such irreversible enzyme inhibitors include,but are not limited to, agents that have reactive functional groups suchas aldehydes, haloalkanes, alkenes, Michael acceptors, phenylsulfonates, or fluorophosphonates that covalently modify nucleophilicgroups such as hydroxyl or sulfhydryl groups, e.g., on serine, cysteine,threonine or tyrosine, to destroy enzyme activity.

In some embodiments, one or more of the therapeutic agents describedherein is administered to a subject who has a viral infection. In someembodiments, the patient has developed disease. In other embodiments,the disease is developing in the patient. In still other embodiments,the patient is asymptomatic. In certain embodiments, the patient issuffering from interstitial lung disease. In yet other embodiments, thepatient evidences a usual interstitial pneumonia pattern onhigh-resolution computed tomography (HRCT). In further embodiments, thepatient has one or more potential risk factors for a viral disease, suchas cigarette smoking, environmental exposure, chronic viral infection,and abnormal gastroesophageal reflux. In other embodiments, the patientis suffering from a lymphoproliferative disease or cancer.

When administered to a patient, a therapeutic agent can be administeredas a component of a composition that comprises a pharmaceuticallyacceptable carrier or excipient. Compositions comprising the compoundcan be administered by absorption through mucocutaneous linings (e.g.,oral, rectal, and intestinal mucosa, etc.). Administration can besystemic or local. Methods of administration include, but are notlimited to, intradermal, intramuscular, intraperitoneal, parenteral,intravenous, subcutaneous, intranasal, epidural, oral, sublingual,intracerebral, intravaginal, transdermal, rectal, by inhalation, ortopical.

In certain embodiments, the therapeutic agent is administered bypulmonary administration, e.g., by use of an inhaler or nebulizer, andformulation with an aerosolizing agent, or via perfusion in afluorocarbon or synthetic pulmonary surfactant. In certain embodiments,a therapeutic agent can be formulated as a suppository, with traditionalbinders and excipients such as triglycerides.

When a therapeutic agent is incorporated for parenteral administrationby injection (e.g., continuous infusion or bolus injection), theformulation for parenteral administration can be in the form of asuspension, solution, emulsion in an oily or aqueous vehicle, and suchformulations can further comprise pharmaceutically necessary additivessuch as one or more stabilizing agents, suspending agents, dispersingagents, and the like. A therapeutic agent can also be in the form of apowder for reconstitution as an injectable formulation.

In yet another embodiment, a therapeutic agent can be delivered in acontrolled-release system or sustained-release system (see, e.g.,Goodson, “Dental Applications” (pp. 115-138) in Medical Applications ofControlled Release, Vol. 2, Applications and Evaluation, R. S. Langerand D. L. Wise eds., CRC Press (1984)). Other controlled orsustained-release systems discussed in the review by Langer, Science249:1527-1533 (1990) can be used.

The compositions can optionally comprise a suitable amount of apharmaceutically acceptable excipient so as to provide the form forproper administration to the subject. Such a pharmaceutical excipientcan be a diluent, suspending agent, solubilizer, binder, disintegrant,preservative, coloring agent, lubricant, and the like. Thepharmaceutical excipient can be a liquid, such as water or an oil,including those of petroleum, animal, vegetable, or synthetic origin,such as peanut oil, soybean oil, mineral oil, sesame oil, and the like.The pharmaceutical excipient can be saline, gum acacia, gelatin, starchpaste, talc, keratin, colloidal silica, urea, and the like. In addition,auxiliary, stabilizing, thickening, lubricating, and coloring agents canbe used. In one embodiment, the pharmaceutically acceptable excipient issterile when administered to the subject. Water is a particularly usefulexcipient when a therapeutic agent is administered intravenously. Salinesolutions and aqueous dextrose and glycerol solutions can also beemployed as liquid excipients, particularly for injectable solutions.Suitable pharmaceutical excipients also include starch, glucose,lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodiumstearate, glycerol monostearate, talc, sodium chloride, dried skim milk,glycerol, propylene glycol, water, ethanol, and the like. Thecompositions, if desired, can also contain minor amounts of wetting oremulsifying agents, or pH buffering agents. Specific examples ofpharmaceutically acceptable carriers and excipients that can be used toformulate oral dosage forms are described in the Handbook ofPharmaceutical Excipients, American Pharmaceutical Association (1986).

The compositions can take the form of solutions, suspensions, emulsions,tablets, pills, pellets, capsules, capsules containing liquids, powders,sustained release formulations, suppositories, emulsions, aerosols,sprays, suspensions, or any other form suitable for use. In oneembodiment, the composition is in the form of a capsule (see, e.g., U.S.Pat. No. 5,698,155). Other examples of suitable pharmaceuticalexcipients are described in Remington's Pharmaceutical Sciences1447-1676 (Alfonso R. Gennaro ed., 19th ed. 1995).

In one embodiment, the therapeutic agent is formulated in accordancewith routine procedures as a composition adapted for oraladministration. A therapeutic agent to be orally delivered can be in theform of tablets, capsules, gelcaps, caplets, lozenges, aqueous or oilysolutions, suspensions, granules, powders, emulsions, syrups, orelixirs, for example. When a therapeutic agent is incorporated into oraltablets, such tablets can be compressed tablets, tablet triturates(e.g., powdered or crushed tablets), enteric-coated tablets,sugar-coated tablets, film-coated tablets, multiply compressed tabletsor multiply layered tablets. Techniques and compositions for makingsolid oral dosage forms are described in Pharmaceutical Dosage Forms:Tablets (Lieberman, Lachman and Schwartz, eds., 2nd ed.) published byMarcel Dekker, Inc. Techniques and compositions for making tablets(compressed and molded), capsules (hard and soft gelatin) and pills arealso described in Remington's Pharmaceutical Sciences 1553-1593 (ArthurOsol, ed., 16th ed., Mack Publishing, Easton, Pa. 1980).

Liquid oral dosage forms include aqueous and nonaqueous solutions,emulsions, suspensions, and solutions and/or suspensions reconstitutedfrom non-effervescent granules, optionally containing one or moresuitable solvents, preservatives, emulsifying agents, suspending agents,diluents, sweeteners, coloring agents, flavoring agents, and the like.Techniques and composition for making liquid oral dosage forms aredescribed in Pharmaceutical Dosage Forms: Disperse Systems, (Lieberman,Rieger and Banker, eds.) published by Marcel Dekker, Inc.

When a therapeutic agent is to be injected parenterally, it can be,e.g., in the form of an isotonic sterile solution. Alternatively, when atherapeutic agent is to be inhaled, it can be formulated into a dryaerosol or can be formulated into an aqueous or partially aqueoussolution.

An orally administered composition can contain one or more agents, forexample, sweetening agents such as fructose, aspartame or saccharin;flavoring agents such as peppermint, oil of wintergreen, or cherry;coloring agents; and preserving agents, to provide a pharmaceuticallypalatable preparation. Moreover, wherein tablet or pill form, thecompositions can be coated to delay disintegration and absorption in thegastrointestinal tract thereby providing a sustained action over anextended period of time. Selectively permeable membranes surrounding anosmotically active driving compound are also suitable for orallyadministered compositions. In these latter platforms, fluid from theenvironment surrounding the capsule is imbibed by the driving compound,which swells to displace the agent or agent composition through anaperture. These delivery platforms can provide an essentially zero orderdelivery profile as opposed to the spiked profiles of immediate releaseformulations. A time-delay material such as glycerol monostearate orglycerol stearate can also be used. Oral compositions can includestandard excipients such as mannitol, lactose, starch, magnesiumstearate, sodium saccharin, cellulose, and magnesium carbonate. In oneembodiment, the excipients are of pharmaceutical grade.

In another embodiment, the therapeutic agent can be formulated forintravenous administration. Typically, compositions for intravenousadministration comprise sterile isotonic aqueous buffer. Wherenecessary, the compositions can also include a solubilizing agent. Atherapeutic agent for intravenous administration can optionally includea local anesthetic such as benzocaine or prilocaine to lessen pain atthe site of the injection. Generally, the ingredients are suppliedeither separately or mixed together in unit dosage form, for example, asa dry lyophilized powder or water-free concentrate in a hermeticallysealed container such as an ampule or sachette indicating the quantityof active agent. Where a therapeutic agent is to be administered byinfusion, it can be dispensed, for example, with an infusion bottlecontaining sterile pharmaceutical grade water or saline. Where atherapeutic agent is administered by injection, an ampule of sterilewater for injection or saline can be provided so that the ingredientscan be mixed prior to administration.

A therapeutic agent can be administered by controlled-release orsustained-release means or by delivery devices that are known to thosein the art. Examples include, but are not limited to, those described inU.S. Pat. Nos. 3,845,770; 3,916,899; 3,536,809; 3,598,123; 4,008,719;5,674,533; 5,059,595; 5,591,767; 5,120,548; 5,073,543; 5,639,476;5,354,556; and 5,733,566. Such dosage forms can be used to providecontrolled or sustained release of one or more active ingredients using,for example, hydroxypropylmethyl cellulose, other polymer matrices,gels, permeable membranes, osmotic systems, multilayer coatings,microparticles, multiparticulates, liposomes, microspheres, or acombination thereof to provide the desired release profile in varyingproportions. Suitable controlled or sustained-release formulations knownto those in the art, including those described herein, can be readilyselected for use with the active ingredients of the invention. Theinvention thus encompasses single unit dosage forms suitable for oraladministration such as, but not limited to, tablets, capsules, gelcaps,and caplets that are adapted for controlled or sustained-release.

Controlled or sustained-release compositions can initially release anamount of a therapeutic agent that promptly produces the desiredtherapeutic or prophylactic effect, and gradually and continuallyrelease other amounts of the therapeutic agent to maintain this level oftherapeutic or prophylactic effect over an extended period of time. Tomaintain a constant level of the therapeutic agent in the body, theagent can be released from the dosage form at a rate that will replacethe amount of agent being metabolized and excreted from the body.Controlled or sustained-release of an active ingredient can bestimulated by various conditions, including but not limited to, changesin pH, changes in temperature, concentration or availability of enzymes,concentration or availability of water, or other physiologicalconditions or compounds.

The amount of therapeutic agent can be determined by standard clinicaltechniques. In addition, in vitro and/or in vivo assays can optionallybe employed to help identify optimal dosage ranges. The precise dose tobe employed will also depend on, e.g., the route of administration andthe seriousness or stage of the condition, and can be decided accordingto the judgment of a practitioner and/or each patient's circumstances.In other examples thereof, variations will necessarily occur dependingupon the weight and physical condition (e.g., hepatic and renalfunction) of the patient being treated, the severity of the symptoms,the frequency of the dosage interval, the presence of any deleteriousside-effects, and the particular agent utilized, among other things.

Administration can be as a single dose or as a divided dose. In oneembodiment, an effective dosage is administered once per month until thedisease is abated. In another embodiment, the effective dosage isadministered once per week, or twice per week or three times per weekuntil the disease is abated. In another embodiment, an effective dosageamount is administered about every 24 h until the disease is abated. Inanother embodiment, an effective dosage amount is administered aboutevery 12 h until the disease is abated. In another embodiment, aneffective dosage amount is administered about every 8 h until thedisease is abated. In another embodiment, an effective dosage amount isadministered about every 6 h until the disease is abated. In anotherembodiment, an effective dosage amount is administered about every 4 huntil the disease is abated. The effective dosage amounts describedherein refer to total amounts administered; that is, if more than oneagent is administered, the effective dosage amounts correspond to thetotal amount administered.

In various embodiments, the therapeutic agent can be administeredtogether with a second therapeutically active agent. In someembodiments, the additional agent is an anti-viral agent, such as aviral entry inhibitor, a viral uncoating inhibitor, an agent thatinhibits release of viruses from cells, an agent that interferes withpost-translational protein modification or with viral protein targeting,or with viral maturation, an antisense compound that is complementary tocritical sections of the viral genome, and the like. Exemplaryanti-viral compounds include, but are not limited to, acyclovir,vidarabine, idoxuridine, brivudine, cytarabine, foscarnet, docosanol,formivirsen, tromantidine, imiquimod, podophyllotoxin, cidofovir,interferon alpha-2b, peginterferon alpha-2a, ribavirin, moroxydine,valacyclovir, trifluridine, and bromovinyldeoxyuridine. In otherembodiments, the additional agent is a chemotherapeutic agent, such asan alkylating agent, an anti-metabolite, an anti-microtubule agent, atopoisomerase inhibitor, or a cytotoxic antibiotic.

In various embodiments, where viral infection leads to autoimmunity in apatient, a tolerizing strategy can be employed. Various tolerizingstrategies can be found, for example, in U.S. patent application Ser.No. 13/871,730.

In one embodiment, a first therapeutic agent is administeredconcurrently with a second therapeutic agent as a single compositioncomprising an effective amount of the first therapeutic agent and aneffective amount of the second therapeutic agent. Alternatively, acomposition comprising an effective amount of a first therapeutic agentand a second composition comprising an effective amount of the secondtherapeutic agent are concurrently administered. In another embodiment,an effective amount of a first therapeutic agent is administered prioror subsequent to administration of an effective amount of the secondtherapeutic agent. In this embodiment, the first therapeutic agent isadministered while the second therapeutic agent exerts its therapeuticeffect, or the second therapeutic agent is administered while the firsttherapeutic agent exerts its therapeutic effect for treating disease.

An effective amount of the second therapeutic agent will be known to theart depending on the agent. However, it is well within the skilledartisan's purview to determine the second therapeutic agent's optimaleffective-amount range. In some embodiments of the invention, where asecond therapeutic agent is administered to a patient for treatment of aviral disease, the minimal effective amount of the compound will be lessthan its minimal effective amount would be where the second therapeuticagent is not administered. In this embodiment, the first therapeuticagent and the second therapeutic agent can act synergistically to treator prevent a condition.

A composition of the invention is prepared by a method comprisingadmixing a therapeutic agent or a pharmaceutically acceptable derivativethereof with a pharmaceutically acceptable carrier or excipient.Admixing can be accomplished using methods known for admixingtherapeutic agents and a pharmaceutically acceptable carrier orexcipient. In one embodiment, the therapeutic agent is present in thecomposition in an effective amount.

5.6. Methods of Preventing Viral Disease

In another embodiment, the present invention relates to methods andcompositions for preventing a viral disease in a subject. In certainembodiments, the viral disease is IPF. In other embodiments, the viraldisease is a lymphoproliferative disease or cancer. In variousembodiments, methods of preventing a viral disease comprise a step ofimmunizing a subject with an immunizing effective amount of an antigen.Accordingly, the present disclosure further relates to a vaccinecomposition for use in the disclosed methods. In certain embodiments,the antigen is an antigenic protein or peptide from a virus. In certainembodiments, the antigen is a protein or peptide from the envelope orcapsid of the virus. In some embodiments, the antigen is selected from avirus envelope associated antigen, a virus latency-associated nuclearantigen, a virus cytoplasmic late antigen, a virus nuclear earlyantigen, and combinations thereof. In certain embodiments, the virus isHerpesvirus saimiri. In other embodiments, the virus is a related virus.

Accordingly, the present disclosure further relates to vaccinecomposition for use in the disclosed methods. In certain embodiments,the antigen is an antigenic protein or peptide from the virus. Incertain embodiments, the antigen is a protein or peptide from the capsidof the virus. In some embodiments, the antigen is selected from a virusmembrane associated antigen, a virus latency-associated nuclear antigen,a virus cytoplasmic late antigen, a virus nuclear early antigen, andcombinations thereof. In certain embodiments, the virus is Herpesvirussaimiri. In other embodiments, the virus is a related virus.

A variety of methods can be used to produce antigenic material forinclusion in vaccine compositions. In certain embodiments, antigenicpeptides can be synthesized based on the complete nucleic acid and/oramino acid sequence of the genome of the virus. In other embodiments,the viral genome can be used as a source of nucleic acids to be usedwith recombinant DNA techniques to generate cells that express proteinsencoded by the viral nucleic acids apart from the rest of the viralgenome. Alternatively, antigenic proteins or peptides can be isolatedfrom viral particles grown in cell culture.

In various embodiments, the vaccine composition comprises an effectiveimmunizing amount of a virus. In some embodiments, the virus is a liveattenuated whole virus. In other embodiments, the virus is aninactivated virus. In particular embodiments, the live whole viruscomprises an inactivating mutation in the genome, e.g., a deletion,substitution or insertion in an endogenous promoter region of anintermediate-early gene. In other particular embodiments, the liveattenuated whole virus is incapable of establishing latent infection. Instill other embodiments, the live vaccine is genetically engineered tolack viral persistence. See, e.g., Wu et al. (2010) Immunology Research48:122-146. In other embodiments, the vaccine comprises recombinantbacteria that express viral antigens. See, e.g., Karem et al. (1997) Jof Gen Virology 78:427-434. Other Herpesvirus vaccine applications andmethods are disclosed, for example, in Burke et al. (1992) CurrentTopics in Microobiology and Immunology 179:137-158; Koelle et al. (2003)Clin Microbiol Rev 16:96-113; Johnston et al. (2011) J ClinInvestigation 121:4600-4609.

In certain embodiments, a vaccine composition for immunization forHerpesvirus saimiri or a related virus can comprise one or more antigensfrom a virus other than Herpesvirus saimiri or a related virus, asinoculation against one Herpesvirus type has been found to protectagainst infection from other Herpesvirus types. See, e.g., Goaster etal., in “Open Access Journal of Clinical Trials” (reporting thatinoculation with a vaccine against varicella zoster also providedbenefits to patients with HSV1 and HSV2 infections). Accordingly, incertain embodiments, the vaccine composition is selected from Zostavax®(Merck), Varivax® (Merck), GEN-003 (Genocea Biosciences) and ACAM529(Sanofi Pasteur).

In certain embodiments, a healthy subject is inoculated. In otherembodiments, a subject who has a viral infection is inoculated. In otherembodiments, a subject who does not have a viral infection, but who hasone or more potential risk factors for viral infection is inoculated. Instill other embodiments, the subject to be inoculated is developing orhas developed a viral disease. In certain embodiments, the subject isasymptomatic. In other embodiments where the vaccine is for Herpesvirussaimiri, the subject to be inoculated is suffering from interstitiallung disease. In yet other embodiments where the vaccine is forHerpesvirus saimiri, the subject to be inoculatd evidences a usualinterstitial pneumonia pattern on high-resolution computed tomography(HRCT).

Administration of the vaccine compositions described herein can be as asingle immunizing effective dose or as a divided immunizing effectivedose. In one embodiment, an immunizing effective dose is administeredonce per month. In another embodiment, the immunizing effective dose isadministered once per year, twice per year, three times per year ormore. In other embodiments, the immunizing effective dose isadministered once every two years, once every three years, once everyfour years or more. In certain embodiments, the vaccine compositions canbe administered in a single immunizing effective dose with boosterinoculations after, e.g., 1 week, 2 weeks, 1 month, 3 months, 6 monthsor one year or more as needed after the initial inoculation. The skilledartisan will recognize that the vaccination schedule is dependent onmany factors, including the amount of anti-viral antibodies present inthe blood of the subject after initial inoculation, the weight andphysical condition of the subject, and the presence of infection and itsseverity, among other things.

Immunization procedures may be carried out by any method known in theart, including but not limited to, intravenous, intramuscular,intraperitoneal, nasal and/or oral administration. The vaccinecompositions described herein can include one or more additional agentsselected from an adjuvant, a preservative, a diluent, a stabilizer, abuffer, a solvent, an inactivating agent, a viral inactivator, anantimicrobial, a tonicity agent, a surfactant, a thickening agent andcombinations thereof. Adjuvants that enhance immunogenic reactionsinclude, but are not limited to, aluminum phosphate, aluminum hydroxide,squalene, an extract of Quillaja saponaria, MF59, QS21, Malp2,incomplete Freund's adjuvant, complete Freund's adjuvant, Alhydrogel®, 3De-O-acylated monophosphoryl lipid A (3D-MPL), Matrix-M™ (Isconova) andcombinations thereof. Other agents that can be included in vaccinecompositions can be found, for example, athttp://www.vaccinesafety.edu/components-Excipients.htm.

5.7. Isolation of Disease-Causing Herpesvirus Sequences

As disclosed in Examples 1 and 2, below, high levels of signal wereobtained using various probes derived from Herpesvirus saimiri that weremodified with Locked Nucleic Acid (LNA) monomers. Probes comprising LNAmonomers form very stable hybrids with target nucleic acids with theresult that probes that are not completely complementary to the viralgenome may still be able to identify the presence of herpesvirus nucleicacids if there is sufficient homology. Accordingly, there is apossibility that the herpesvirus present in the IPF specimens assayed inExamples 1 and 2 is a variant of Herpesvirus saimiri having mutationsand/or alterations in the genome that confer on the virus the ability togrow in humans. Furthermore, there is a possibility that the Herpesviruspresent in IPF patients is not Herpesvirus saimiri itself, but is anundescribed but related gamma herpesvirus that shares extensive homologywith Herpesvirus saimiri.

To gather further information regarding the viral infectious agent inIPF, tissue samples were tested with probes using unmodified nucleotidesrather than LNA nucleotides to insure that any positive results for thepresence of the virus were dictated by the complementarity of the probeand not by affinity enhancing modifications such as LNA. As described inExample 9, below, larger probes composed of normal bases were made bycreating clones that contained the Herpesvirus saimiri sequences for thepolymerase gene (1,826 nucleotides; SEQ ID NO: 11), the Terminal Repeatregion (1,383 nucleotides; SEQ ID NO: 12), the IL-17 gene (853nucleotides; SEQ ID NO: 13) and the STP gene (1,232 nucleotides; SEQ IDNO: 14). Plasmid DNA from these clones was nick-translated and labeledwith biotin-labeled dUTP (“biotin-labeled probes”) and hybridized underthe same conditions as the LNA probes in the experiments described inExamples 1 and 2. See Example 10, below. As seen in FIG. 10, the largerunmodified probes gave substantially the same results as the LNA probesin Examples 1 and 2. Specifically, the biotin-labeled probes showedstrong hybridization to epithelial cells in IPF samples. Accordingly, insitu hybridization with LNA probes as reported in Examples 1 and 2 andwith the biotin-labled probes as reported in Example 10 demonstrate thatboth types of probes target viral sequences present in IPF samples.

Nevertheless, these experiments do not clearly establish whether thereis total or partial homology between the Herpesvirus saimiri derivedprobes and the target sequences in IPF samples. To establish the degreeof homology of the probes with target sequences in the IPF samples,hybridizations were carried out with a pool of the four biotin-labeledprobes described above (SEQ ID NOs: 11-14) followed by washing withvarying degrees of stringency. For comparison, the digoxigenin labeledLNA STP probes from Example 1 were also used with high stringency (50°C.) washes. As described in Example 11, three different washingconditions were used for the biotin-labeled probes, “high stringency”with 0.1×SSC at 50° C.; “low stringency” with 0.1×SSC at 4° C. and “verylow stringency” with 1×SSC at 4° C. The results of these experiments areshown in Table 3. When the biotin-labeled probes were used, threespecimens (137431, 7480 and 71706) showed a difference in hybridizationin only one level between low stringency and very high stringency, andtwo samples (994326 and 205601) showed a difference in hybridization intwo levels—3/0 to 1/0 for 994326 and 2/0 to 0/0 for 205601—indicating apossibility that there are sequence differences between thebiotin-labeled probes and the herpesvirus sequences in the IPF samples.In contrast, the LNA probes continued to show high signal levels for allof the tested IPF samples, even after a high stringency wash. Inaddition to the IPF specimens, some of the other diseases that have nowbeen shown to be associated with Herpesvirus saimiri were also tested inthe same manner as described in Example 12. The results are shown inTable 3. Interestingly, a consistent loss of signal was observed whenusing the biotin-labeled probes under high stringency conditions ascompared to low stringency conditions. This result may indicate that theclinical samples are not infected by Herpesvirus saimiri, but by one ormore novel viruses.

It should be pointed out that, even considering the results indicatingthat there is not a perfect match between Herpesvirus saimiri sequencesand the target sequences in the clinical samples, Herpesvirus probes canbe used under proper hybridization and washing conditions to efficientlybind to related gammavirus sequences in clinical specimens. Moresensitive detection may be developed by examining the Herpesvirussequences in IPF and other diseases that generate signals withHerpesvirus saimiri probes. Once these sequences are determined, assayscan be further optimized by redesigning probes such that they are morehighly complementary to viral sequences in the clinical specimens. Theuse of optimized probes will allow for the detection of viral sequencesin clinical specimens using more stringent hybridization and washingconditions, thereby potentially reducing background signal fromnon-target sequences. The present invention allows such optimized probesto be designed according to the experimental results described hereinrelating to the reactivity of Herpesvirus saimiri probes. These resultsallow a ‘tag’ to be used for screening clones from a library of nucleicacids made from infected cells. The principle that limited homologybetween viruses can be used as a marker for isolating novel viruses fromclinical samples is well established, as it has been done to identifyand clone human papilloma viruses. Specifically, numerous types of HPVwere identified and cloned using a “leapfrog” technique with a probedesigned for a known HPV type used to isolate novel but related familymembers. For instance, HPV6b was used to identify HPV11 at lowstringency in a phage library (Gissman et al., 1982 J Virol 44; 393);labeled HPV11 was then later used to isolate a clone of HPV16 (Durst etal., 1983 Proc Nat Acd Sci (USA) 80; 3812-3815) and in turn, lowstringency probing with labeled HPV16 allowed isolation of a clone ofHPV33 (Beaudenon et al., 1986 Nature 321 246-249). In a similar fashion,the clone for HPV18 was identified and isolated using a mixture of HPVs8, 9, 10 and 11 (Boshart et al., 1984 EMBO Journal 3; 1151-1157), and apool of HPV types were used to isolate HPV31 (Lorincz et al., 1986 JVirol 58; 225-229) and HPV51 (Nuovo et al., 1988 J Virol 62; 1452-55).In addition, limited homology can also be used on a microscale wherecertain segments of a virus tend to be more conserved. Thus again usingthe example of HPV, after information on a number of sequences ofvarious types had accumulated, consensus primers were developed thatcould amplify a large variety of different HPV types by PCR. Theconsensus primers that have been used most frequently to identify otherHPVs are the MY09/MY10 pair (Manos et al., 1989 Cancer Cells 7; 209-214)and the GP5+/GP6+ pair (Husman et al., 1995 J Gen Virol 76; 1057-1062),which are both derived from conserved sequences in the HPV L1 gene.

The knowledge that there is a herpesvirus in IPF that has homology withvarious DNA probes derived from Herpesvirus saimiri allows for isolationof all or a portion of the genomes of the virus that is present inpatients using various known methods. For instance, similar to what hasbeen described for HPV, primer sets have been described that aresufficiently generic that they can amplify a number of novel gammaherpesviruses from tissue samples from a variety of organisms by takingadvantage of a relative conservatism in the DNA polymerase, glycoproteinB and/or terminase genes among various members of the gamma herpesvirusfamily. (Chmielewicz, et al., 2001 Virus Research 75; 87-94; Ehlers etal., 2007 J Virol 81; 8091-8100; Ehlers et al., 2008 J Virol 282;3509-3516). Animals that were successfully used to obtain sequences ofnew gammaviruses were phylogenetically very disparate and includedrepresentatives of Primates (gorilla), Artiodactyla (chamois and pigmyhippopotamus), Perissodactyls (zebra and tapir), Proboscidea (Asianelephant) and carnivores (lion and spotted hyena). Not surprisingly, theviral sequences between the generic primers echoed the phylogenticdistances between the hosts. (Ehlers et al., 2008). Consequently, in oneembodiment, these primer sets can be used to obtain sequences fromclinical samples that are suitable for identification of thephylogenetic relationship of the gamma herpesvirus in IPF patients tothe known sequence of Herpesvirus saimiri, where the patient-derivedviral sequence is a) identical to Herpesvirus saimiri, b) essentiallythe same as Herpesvirus saimiri with some sequence variation or c) anovel virus related to Herpesvirus saimiri sufficiently similar suchthat probes derived from Herpesvirus saimiri can display stable probebinding in clinical samples. The connectivity of the IPF pathogen tosequences that are more distant from the Herpesvirus saimiri genome canthen be validated using these new sequences to make labeled probes thatcan be reapplied to clinical specimens previously showing positivitywith the Herpesvirus saimiri probes.

In some embodiments, semi-generic primers are used to isolate theinfecting gamma herpesvirus. In this approach, recognition of thesimilarity between Herpesvirus saimiri and the herpesvirus resident inIPF patients implies that it is unlikely to be a distantly-related gammaherpesvirus. As such, instead of using primers that are designed toamplify any and all gammaviruses, a more selective approach can be usedby aligning the sequences of, for example, the polymerase genes ingammaviruses that are phylogenetically close and designing primers thatwill amplify all polymerase genes in the subgroup. In theory, thisapproach is more selective and more efficient because primers designedusing this approach will have fewer mismatches with the infectingpathogen that a pan-gammavirus primer set.

In other embodiments, subtractive hybridization is used to eliminatemuch of the chromosomal DNA or RNA that is present in a nucleic acidpreparation made from a clinical specimen from an IPF patient. A briefreview of this method for isolation of novel viruses is set forth inMuerhoff et al. (1997) J Med Virol 53: 96-103. An example of thistechnique as applied to HVS is described in Knappe et al. (2000) J Vir74:3881-3887 where cDNA fragments were searched for genes expressed inHVS-transformed lymphocytes but not in untransformed cells. The power ofthe method can be seen in that, among 399 sequenced clones, 280 wereviral DNA clones and 119 were cellular cDNA clones. In this particularinstance, Knappe et al. were focused on the nature and identity of thecellular cDNA clones, but the fact that they achieved such a high numberof viral clones from the HVS-infected transformants as a byproductimplies that similar results can be achieved when using IPF and normalcells instead of infected and uninfected lymphocytes.

In yet other embodiments, positive selection is used to isolate a virus.For example, LNA probes that were used against the TER and STP regionsof Herpesvirus saimiri were discovered to be specific and able to bindefficiently to the viral sequences present in IPF patients, as shown inExamples 1 and 2. As such, the same LNA sequences used with digoxigeninlabels can be sythesized with a biotin label at a terminus and, afterhybridization with IPF DNA (STP Or TER) or mRNA (STP), bound nucleicacids can be obtained with either a streptavidin column or streptavidinbeads. The captured nucleic acids can then be used as a library ofclones to be probed with LNA probes or other Herpesvirus saimirisequences. A similar approach can also be taken with LNA probes that aredesigned for other genome segments.

In various embodiments, classic shotgun cloning of a library of eitherDNA or cDNA from IPF patients and screening of clones using probesderived from either a portion or the entire genome of Herpesvirussaimiri can be used to isolate the infecting virus. This method providesno bias either for or against clones and identification is strictly dueto the presence of homology with Herpesvirus saimiri. Since there is alarge amount of chromosomal DNA in any virus-infected cell, asequence-independent enrichment process can used to increase the portionof viral DNA as compared to host DNA. In certain embodiments, enrichmentcan be accomplished using a Hirt procedure (Hirt (1967) J Mol Biol26:365-369) that selectively allows episomal DNA to remain in solutionwhile most of the chromosomal DNA is precipitated with detergent. Thismethod has been successful when used with herpesviruses, even though theviral genome is large (130-150 kb) (Pater et al. (1976) Virology 75;481-483; Rosenthal et al. (1983) Intervirology 19; 113-120; Eizuru etal. (1984) J Clin Microbiol 20; 1012-1014). Other techniques forsequence-independent enrichment include separation of viral-proteincomplexes (Pignatti et al. (1979) Virology 93; 260-264) and isolation ofviral particles (Kintner and Brandt (1994) J Vir Methods 189-196). Lowstringency hybridization with HVS probes should allow identification andisolation of clones with homology with HVS that have been linked to thevarious diseases previously described. Sequencing of these probes shouldclarify the relationship of the herpesvirus in the clinical samples withthe Herpesvirus saimiri sequence.

5.8. Mouse Model of IPF

In certain embodiments, the various methods described herein can becarried out using an animal model of disease in lieu of, or in additionto, patient samples. Accordingly, in some embodiments the variousmethods described herein can be carried out using a mouse model, such asthe mouse model described by Pierce et al. (2007) Am J Pathology170:1152-1164. This mouse model is achieved by intravenously injectinghuman primary fibroblasts from IPF patient lung biopsies into SevereCombined Immunodifficient (“SCID”) mice. The human cells migrate to thelungs and cause patchy interstitial fibrosis upon examination at 35 and63 days after injection. In contrast, fibroblasts from normal donors donot induce fibrotic change in lung structure when injected into SCIDmice. This mouse model has been used to investigate the roles of CCligand 21 and CCR7 (Pierce et al. 2007) and the TL9 receptor (Trujilloet al. (2010) Sci Transl Med 2(57): 57ra82) in pulmonary fibrosis, aswell as the exacerbation of fibrosis by CpG-oligodeoxynucleotide(Hogaboam et al. (2012) Fibrinogen & Tissue Repair 5(Suppl. 1):S3).Furthermore, transfer of fibroblasts from IPF patients to a SCID mousehost should also convey the Herpesvirus causative agent of IPF.

Although the SCID mouse model of IPF does not totally recapitulate thedisease, the observation that human primary fibroblasts from IPFpatients colonize the mouse lung and are associated with development offibrotic lung tissue offers an easily manipulated and inexpensive systemfor further research into disease markers, compositions for detection ofdisease, and identification of therapeutic agents. Accordingly, in someembodiments, the SCID mouse model is used to identify and optimizeprobes and primers for detection of viral nucleic acids and/oramplification of nucleic acids from patient samples. In one particularembodiment, original cells taken from a human patient after fibrosis hasbeen established are expanded in vivo, and the mouse lungs are used as asource of tissues for examination of Herpesvirus sequences, either by insitu hybridization and/or by extraction of nucleic acids from the cellsand tissues. In various embodiments, markers of human cells are used todistinguish between mouse cells and human cells in order to determine ifviral sequences and/or viral protein expression are transferred from thetransplanted patient cells to the cells of the murine host. In variousembodiments, the extracted nucleic acids are used for isolation andamplification of viral nucleic acid sequences by any means previouslydescribed.

In various embodiments, the SCID mouse model of IPF is used fordetecting the presence of various disease markers of IPF that are notreadily assayed in a human patient. In certain embodiments, the mousemodel is utilized for detecting IPF markers not only in lung tissues orbronchiolar lavage, but also in blood or other tissues that are moreeasily collected from a human patient than lung tissue. In variousembodiments, the mouse model is used for identifying disease-drivenphysiological changes in tissues that are not normally associated withIPF, or detecting disease-driven physiological changes associated with aparticular stage of the disease, or associated with rapidly progressingdisease versus slowly progressing disease.

The collection of human lung samples by needle biopsy is invasive andpresents many risks, including lung collapse, respiratory failure andbleeding, which are more common in patients ages 60 to 69 (IPF usuallypresents in adults over 50 years of age), smokers, and patients withchronic obstructive pulmonary disease (COPD). See Soylemez Weiner et al.(2011) Annals of Internal Medicine 155(3):137-144. Accordingly, in stillother embodiments, the SCID mouse model is used in assays that require anegative control in lieu of a lung biopsy from a human subject that doesnot have IPF. In these embodiments, the IPF mouse model is the positivecontrol and a non-infected SCID mouse is the negative control.

In still other embodiments, the SCID mouse model is used to identifytherapeutic agents for the treatment of IPF, such as those described inSection 6.5, above. In particular embodiments, by virtue of itsinability to make antibodies, the SCID mouse model is used to determinethe efficacy of therapeutic antibodies, such as antibodies to viral geneproducts whose expression is correlated with IPF. Accordingly, in someembodiments, the SCID mouse model is used to determine the therapeuticefficacy of a viral IL-17 antibody, a viral IL-10 antibody or a virallatency-associated nuclear antigen antibody. In other embodiments themouse model is used to determine the therapeutic efficacy of an antibodyselected from an anti-TGF-β antibody, an anti-IL-23 antibody, and ananti-IL-1β antibody. In still other embodiments, the mouse model is usedto determine the therapeutic efficacy of an antibody selected from ananti-DHFR antibody, an anti-cyclin D antibody, and an anti-thymidylatesynthase antibody. Furthermore, although the identification andevaluation of therapeutic agents that target viral replication and/orpropagation can be carried out in virus infected human cell culture, theability to administer such agents in an in vivo model of disease shouldgenerate results that have a likelier chance of success when positivecandidates are later tested in humans.

6. EXAMPLES

This section describes the various different working examples that willbe used to highlight the features of the invention(s).

Example 1: Hybridization with LNA Oligonucleotide Probes from STP Regionof Herpesvirus Saimiri

Detection of Herpesvirus saimiri sequences in paraffin embedded formalinfixed samples from IPF patients was carried out by in situ hybridizationwith oligonucleotides probes according to methods described in Nuovo etal. (2010) Methods 52:307-315. Formalin fixed paraffin embedded tissuesamples from 22 IPF patients in which sufficient tissue was availablefor molecular studies were obtained from archived files. The mean age ofthe patients was 56.6 years (SEM=2.5 years), 14 were men and 8 werewomen. Evaluation of the hematoxylin and eosin stains of these tissuesconfirmed the heterogeneous histologic findings of usual interstitialpneumonitis. In each IPF case, no etiology or underlying disease statecould be identified for the patient's illness.

In brief, slides were pre-treated for 4 minutes with Proteinase K(Ventana Medical Systems) and then hybridization was carried out with a5 femtomole/μL solution of labeled probes. The probes used for thisprocess were LNA analogues with digoxigenin labels at their 5′ ends(Exiqon) and were derived from the sequence of the Herpesvirus saimiriSTP gene of the C488 strain of Herpesvirus saimiri (Albrecht et al.(1992) J Virology 66:5047-5058).

Oligo #1 (SEQ ID NO: 5) 5′-CTCTAAGCACAGGGGCACAG-3′ Oligo #2(SEQ ID NO: 6) 5′-CTACGCAGAAGTCGGAAGCC-3′

The oligonucleotides were used as labeled probes (SEQ ID NO: 5 and SEQID NO: 6). Their relative locations can be found using Genbank Accession# M28071 for the STP sequence. Probe/target complex was detected withalkaline phosphatase-anti-digoxigenin conjugate reacting with nitrobluetetrazolium and bromochloroindolyl phosphate (NBT/BCIP) forming aninsoluble blue precipitate. Negative cells were counterstained withnuclear fast red. Negative controls included the omission of probes,oligonucleotides with scrambled probe sequences and the use of specimensfrom non-IPF lung fibrosis patients. Hybridization and detection withthese probes gave positive readings in the IPF samples as shown in FIG.1A where intense cellular staining with the Herpesvirus saimiri DNAprobes can be seen at the arrow indicator. For comparison, a lung cancerspecimen is shown in FIG. 1B, indicating a lack of any staining with theHerpesvirus saimiri-specific labeled probes.

Example 2: Hybridization with LNA Oligonucleotides from STP and TER

In order to rule out the possibility of an artifact giving falsepositives, another set of digoxigenin-labeled LNA probes (SEQ ID NO: 7;SEQ ID NO: 8) were designed to specifically bind to a different portionof the Herpesvirus saimiri genome, the 1,444 nucleotide Terminal Repeat(TER) sequence of C488 (Bankier et al. (1985) J Virology 55:133-139).

Oligo #3 (SEQ ID NO: 7) 5′-GCCGCCTCAGAATTTTAGCA-3′ Oligo #4(SEQ ID NO: 8) 5′-CTCTGCGTGAAGCACAGTGC-3′

These oligonucleotides were used as labeled probes. Their relativelocations can be found using Genbank Accession # K03361 for thereference sequence. In FIG. 2, two serial sections of a specimen weretested with the STP pair (SEQ ID NO:5 and SEQ ID NO:6, FIG. 2A) or theTER pair (SEQ ID NO:7 and SEQ ID NO:8, FIG. 2B). Hybridization wasaccomplished with both sets of labeled probes and the signal from eachset was generated in the same areas of the biopsy section, confirmingthat these are areas of viral infection. As a further control, other mixand match experiments were carried out using serial sections with theSTP or TER probe sets in individual hybridization reactions, and 5 outof 5 specimens were positive for each set (data not shown). In anothervariation, either the (+) strand STP probe or the (−) strand STP probewas individually used, and 5 out of 5 specimens gave the same results(data not shown).

Twenty-two IPF samples were tested, and all specimens scored positivefor Herpesvirus saimiri DNA. A number of pulmonary samples from non-IPFpatients were tested as negative controls. These specimens included 7cases of scar adenocarcinoma of the lung, 9 cases of lung fibrosisassociated with emphysema and 9 cases of nonspecific interstitialpneumonia (NSIP) associated with known viral infection, includingmeasles (1 case), adenovirus (3 cases), hantavirus (3 cases) androtavirus (2 cases). All 25 of these non-IPF specimens were negative forhybridization of the Herpesvirus saimiri probes, demonstrating a strongnegative correlation. The majority of the cases were also tested usingbiotinylated DNA probes (Enzo Biochem) for other viruses, includingEpstein-Barr Virus (EBV) cytomegalovirus (CMV) and Herpes simplex virustypes I and II (HSV-I/II) and all were negative for the presence ofthese viruses.

The Herpesvirus saimiri DNA distribution closely paralleled thehistopathology of IPF (FIG. 3A-3C). Herpesvirus saimiri nucleic acidswere evident in the regenerating epithelial cells in the areas of activeIPF (FIGS. 3D, 3G and 3H). Rare viral DNA-positive pneumocytes were seenin the histologically unremarkable areas of the IPF lung sections (FIG.3E) and various positive cells were not in evidence in the areas ofend-stage fibrosis of IPF which lacked epithelial cells (data notshown), or in the regenerating epithelial cells of interstitialpneumonitis of known etiology (FIG. 3F). Although scattered interstitialcells with the cytological appearance of macrophages as well as rareendothelial cells were positive for viral DNA, over 95% of the cellspositive for viral DNA were regenerating epithelial cells.

Example 3: Detection of IL-17

The discovery that there is active infection by Herpesvirus saimiri inepithelial cells of IPF patients offers an explanation for the resultsof earlier nucleic acid and proteins studies showing insignificantchanges in the amount of IL-17 in IPF patients, which contrasted to theresults of Nuovo et al. (2012), which showed high levels of expressionof IL-17 in IPF specimens in replicating epithelial cells, a type ofcell unassociated with IL-17 expression. This paradox can now beresolved in that previous microarray, protein array and ELISA resultsdid not show evidence of any profound changes in human IL-17 whereas theNuovo et al. (2012) results are a result of detection of viral IL-17coded by Herpesvirus saimiri.

FIG. 4 shows comparisons of the human and viral sequences for IL-17 forboth the protein (FIG. 4A) and nucleic acid (FIG. 4B) sequences. Theprotein sequence comparison (FIG. 4A) shows that there are a number ofepitopes that appear in only the human version of IL-17 (SEQ ID NO:1).Accordingly, if previous antibody studies used a monoclonal antibody (asin ELISA and protein arrays) specific for one of these human epitopes,the viral form of IL-17 (SEQ ID NO:2) would not have been detected bythe antibody. The same is true for the nucleic acid comparison, wherethere are numerous segments that, if used as microarray elements, wouldbe complementary to only the human version of IL-17 (SEQ ID NO:3). Withregard to this point, when microarrays are designed, the usual criteriafor the choice of sequences for capture elements is a lack of identitywith other similar sequences. Consequently, in the microarray studies ofnucleic acids in IPF patients, measurements of human IL-17 nucleic acidswould have been investigated, but no probes to the viral IL-17 nucleicacids were likely used in these studies. On the other hand, Nuovo usedpolyclonal antibodies, which likely recognized multiple epitopes in theviral IL-17 that are shared by both human and viral proteins, andtherefore, would be recognized by the polyclonal antibodies. Thepresence of conserved segments that comprise identical sequences can beseen in the comparison of FIG. 4. As such, viral expression of IL-17 inthe cells of IPF patient specimens was detected by Nuovo by use of thepolyclonal antibodies.

Example 4: Immunohistochemistry of Viral Proteins in IPF and Non-IPFLung Tissue

As noted above for IL-17, one of the properties of the gammaherpesvirusfamily is the “adoption′” or “pirating” of host genes into the viralgenome. Consequently, given that Herpesvirus saimiri DNA was detected inIPF samples and that the results with an anti-IL-17 polyclonal antibodywere interpreted as detection of virally encoded IL-17, other viralhomologues coded by Herpesvirus saimiri should also be detectable in theIPF specimens. Accordingly, histochemical analysis was carried out asdescribed in Nuovo et al. (2010) Methods 52:307-315 using polyclonalantibodies to dihydrofolate reductase (DHFR), thymidine synthase (TS)and cyclin D1. Relative amino acid identities with the human equivalentsare respectively 83%, 66% and 25% (Reviewed in Fickenscher andFleckenstein (2001) Phil Trans R Soc Lond B Biol Sci. 356(1408):545-67).The similarity between the viral and human genes should be sufficientfor some shared epitopes in the viral proteins to be recognized bypolyclonal antibodies against the human gene products.

In brief, the automated Benchmark LT immunohistochemistry system wasused with primary antibodies from ABCAM. An equal number of controlswere also tested for each of these proteins using immunohistochemistry.Tissue specimens from this study are shown in FIG. 5. FIG. 5A-5C showthe histologic distribution of cyclin D1 in IPF as determined byimmunohistochemistry (signal fast red with hematoxylin counterstain).FIG. 5A shows that protein was expressed in the majority of regeneratingepithelial cells in the areas of active fibrosis (FIG. 5A, 100×) and,like the viral DNA, in rare alveolar lining cells in the histologicallynormal areas in the IPF lung (FIG. 5B, 400×). At higher magnification inthe active fibrosis areas the strong signal for cyclin D1 was foundexclusively in the regenerating epithelial cells (FIG. 5C, 400×).Another viral homologue, dihydrofolate reductase (FIG. 5D, 100×) showsthe same topographic pattern as cyclin D1 and viral DNA and, similarly,shows rare positive alveolar lining cells in the adjacent histologicallynormal lung (FIG. 5E, 400×). FIG. 5F shows a strong signal forthymidylate synthase in a region with marked interstitial fibrosis inIPF (400×, DAB signal, hematoxylin counterstain). Both dihydrofolatereductase and cyclin D1 are commonly found in the malignant epithelia oflung cancer (FIGS. 5G and 5H, respectively, each at 200× with fast redsignal and hematoxylin counterstain-large arrows). However, unlike theIPF samples, these proteins were not evident in the subjoining areas ofthe lung that showed active fibrosis and regenerating serpentine glands(small arrows).

Example 5: Histochemical Testing for Non-HVS Viruses

Immunohistochemical analyses were carried out by probing for the latentmembrane protein (LMP) of EBV, the latent nuclear antigen (LNA-1) ofKSHV, and CMV proteins 8B1.2, 1G5.2, and 2D4.2, respectivelyrepresenting immediate early, early, and late antigens of CMV. Noviruses were detected by these methods. (Data not shown)

Example 6: Co-Localization of HVS DNA and Protein Targets

To show that there is a direct connection between the presence ofHerpesvirus saimiri DNA and expression of viral homologues coded by thevirus, experiments were carried out that simultaneously detected thepresence of DNA and protein targets in the same specimen. Methods forthis simultaneous detection have been described in Nuovo et al. (2009)Nature Protocols 4:107-115. Briefly, computer-based analysis by theNuance system (Caliper) separates each chromogenic spectral signal,converts it to a fluorescent signal, then mixes the two and indicates ifcells contain the two targets of interest.

Results for this analysis are shown in FIG. 6 and indicate thatexpression of IL-17, cyclin D and thymidylate synthase are directlycorrelated with the presence of Herpesvirus saimiri in the cells. Noteespecially that FIG. 6E-6H show the same groups of cell in subjacentserial sections.

Example 7: Detection of HVS in Patients with Castleman's Disease

Thirteen HIV-1 negative patients suffering from idiopathic Castleman'sdisease and 13 control patients (which included tissues from benignlymph nodes, and four patients with various neoplastic diseasesincluding Burkitt's lymphoma, oral hairy leukoplakia and other diseases)were tested for the presence of Herpesvirus saimiri. Of the Castleman'sdisease patients examined, 9 were men and 4 were women, and the mean agewas 45.5 years. Lymphoproliferative Castleman's tumors ranged from 3.2cm to 8.5 cm (mean 6.0 cm) and 12 of the tumors were mediastinal orretroperitoneal. Three cases were multicentric and 10 were unicentric.

All patients and control patients were tested for the presence of HVSDNA in formalin fixed paraffin embedded tissue samples using in situhybridization with STP probes (SEQ ID NO: 5 and SEQ ID NO: 6 in Example1). Five cases were tested with TER probes (SEQ ID NO: 7 and SEQ ID NO:8 in Example 2), and all cases were tested with probes directed againsttwo of the major Herpesvirus saimiri specific U rich noncoding regionsmall RNA molecules (Cazalla et al. (2010) Science 328:1563-66) andhaving the sequences:

Oligo #5 (SEQ ID NO: 9) 5′-TATTTACACCCAGTACCTACAAAAATT-3′ Oligo #6(SEQ ID NO: 10) 5′-TAAATAAATATGTAGTGT-3′

These probes were also LNA modified and 5′ tagged with digoxigenin.

Using in situ analysis, patient tissues were further characterized byscreening for expression of cyclin D and IL-17.

As set forth in Table 1, below, all 13 of the Castleman's diseasepatients were positive for HVS DNA using the STP and U rich noncodingregion small RNA probes, whereas normally, only 4-7% of adult humans arepositive for HVS DNA. In addition, as set forth in Table 2, below, 0 of13 control patients were positive for HVS DNA. Viral nucleic acids werelocalized in patients to the majority of B-cells in the expandedgerminal centers/mantle zone that is typical of Castleman's disease,while the interfollicular zone (“T cell zone”) was negative for virus.See FIG. 7A-7B, 7H. Identification of infected cells as B-cells wasconfirmed by the presence of CD20 on the cells. FIG. 7C. Viral infectionwas non-lytic based on the low percentage of HVS+ cells expressing viralIL-17. See FIG. 7D. T-cells were localized primarily to the zone betweenthe expanded germinal centers/hyperplastic mantle zone and had high IL-6expression induced by infected B-cells. See FIG. 7E-7F. Infected B-cellswere found to be negative for both CD3 and IL-6, FIG. 7G. Most B-cellsin tissues of Castleman's patients are positive for Herpesvirus saimiriU-rich noncoding RNA which is indicative of a latent infection. Thus,idiopathic Castleman's disease (unicentric and multicentric forms) isassociated with a massive, non-lytic HVS infection of B-cells thatinduces IL-6 production in adjacent T-cells. HVS proteins were notabundant in the affected tissues of Castleman's disease patients.

TABLE 1 Presence of Herpesvirus saimiri in 13/13 Castleman's diseasepatients Herpesvirus Herpesvirus saimiri saimiri Case STP probe URNACyclin D1 IL-17 Castleman 1  Positive 3+ Positive 3+ 1+ 1+ Castleman 2 Positive 3+ 1+ 1+ Castleman 3  Positive 3+ Positive 3+ 1+ Castleman 4 Positive 3+ 1+ 1+ Castleman 5  Positive 3+ Positive 3+ 1+ 1+ Castleman6  Positive 3+ 1+ 1+ Castleman 7  Positive 3+ Positive 3+ 1+ 1+Castleman 8  Positive 3+ Positive 3+ 1+ 1+ Castleman 9  Positive 3+Positive 3+ 1+ 1+ Castleman 10 Positive 3+ 1+ 1+ Castleman 11 Positive3+ 1+ 1+ Castleman 12 Positive 3+ Positive 3+ 1+ Castleman 13 Positive3+ Positive 3+ 1+

TABLE 2 Control Subjects 0/13 for Herpesvirus saimiri HerpesvirusHerpesvirus saimiri saimiri Case STP probe URNA Cyclin D1 IL-17Burkitt's lymphoma Negative Negative Endothelial 0 Oral hairyleukoplakia Negative 0 0 AIDS-related DLBCL Negative Negative HHV8+Castleman's Negative 0 0 Lymph node benign Negative Negative Endothelial0 Tonsil benign Negative Negative 0 0 Spleen benign Negative Endothelial0 Lymph node benign Negative Negative Endothelial 0 Lymph node benignNegative Negative 0   1+ Lymph node benign Negative Negative Endothelial0 Lymph node benign Negative Negative —   1+ Lymph node benign NegativeNegative Endothelial 0 Lymph node benign Negative Negative Endothelial 0

Example 8: Detection of HVS in Patients with Cancer

All testing described in this example was done using formalin fixedparaffin embedded tissue samples using in situ hybridization. Testing of4 mediastinal, 2 retroperitoneal, 8 head/neck and 4 pericolic B-celllymphoma tissues revealed that HVS DNA was present in 6 out of 12mediastinal and retroperitoneal lymphoma samples, but was not present inany of the other 12 B-cell lymphomas (head/neck and pericolic).Forty-six thymomas were analyzed for HVS using STP and U-RNA probes.Twenty-three of 46 thymoma samples (50%) were positive for HVS DNA,while 0/19 samples of normal thymus tissues were positive for HVS DNA.Two thymoma samples from different patients that are HVS+ are shown inFIG. 8A-8B.

Analysis of other markers showed that 29/46 (63%) of thymoma sampleswere positive for CD20, 29/46 (63%) of thymoma samples were positive forIL-17 (FIG. 8B) (whereas 5/15 (33%) of normal thymus samples werepositive for IL-17), 34/46 (73%) of thymoma samples were positive forcyclin D (FIG. 8C) (whereas 6/15 (40%) of normal thymus samples werepositive for cyclin D), and 43/46 (93%) of thymoma samples were positivefor keratin. As shown in FIG. 8C-8D, relatively few thymoma cells testedpositive for viral IL-17 or viral cyclin D1.

Two retroperitoneal liposarcomas were analyzed for HVS DNA using STPprobes (SEQ ID NO: 5 and SEQ ID NO: 6 in Example 1) and TER probes (SEQID NO: 7 and SEQ ID NO: 8 in Example 2), and both were positive for thevirus. (FIG. 9A-9B) As shown in FIG. 9A, in one sample, HVS+ cells hadlocalization of signal in the nucleus, which is typical of herpesvirusinfections in general. In addition, eighteen gastrointestinal stromalsarcoma samples were tested using STP probes (SEQ ID NO: 5 and SEQ IDNO: 6 in Example 1) and TER probes (SEQ ID NO: 7 and SEQ ID NO: 8 inExample 2) and 2 samples (not retroperitoneal) were positive for HVSDNA. (FIG. 9A-9B) Finally, 16 sarcomas that were not retroperitoneal ormediastinal (leiomyosarcoma, antiosarcoma, chondrosarcoma, and synovialsarcoma) were tested for the presence of HVS using STP probes (SEQ IDNO: 5 and SEQ ID NO: 6 in Example 1) and TER probes (SEQ ID NO: 7 andSEQ ID NO: 8 in Example 2), and were found to be HVS negative.

Example 9: Design and Synthesis of Biotinylated Probes for HerpesvirusSaimiri

Viral DNA sequences were synthesized to make probes for hybridizing toIPF patient samples. The polymerase gene, terminal repeats, viral IL-17gene and viral StpA gene of Herpesvirus saimiri were synthesized byGenscript, and inserted into the cloning vector pUC57(http://www.genscript.com/vector/SD1176-pUC57_plasmid_DNA.html).

The polymerase probe (GenBank: AJ410493.1) has the sequence:

(SEQ ID NO: 11) GAATTCCAAACAGACATAATACCTAATGGAACAGTGTTGAAACTACTTGGAAGAACACTAGAGGGTGCGAGCGTATGTGTTAACGTGTTTGGACAAAGAAATTACTTTTATGTTAAAGTTCCGGAAGGTGGCAACATAACCTATCTTATGAAACAAGCTTTGAATGAAAAATTTAGCCCATCTTGTGCATACCAAACTGAAGCAGTAAAAAAGAAGATACTATCTAGATATGATCCAAAAGAACATGATGTTTTTAAAGTGACAGTGTCTTCTTCTCTTTCTGTTTATAAAATATCAGATTCTTTAGTGTCTAATGGTTGTGAAGTTTTTGAAACAAATGTAGATGCTATAAGAAGATTTGTAATTGATAACAACTTCTCTACATTTGGTTGGTACACATGTAAGTCTGCATGTCCTCGAATCACAAATAGAGACTCTCATACTGACATTGAGTTTGACTGCGGGTACTATGACTTGGAATTTCATGCAGATAGAACAGAATGGCCACCTTACAACATAATGTCTTTTGATATAGAATGTATAGGAGAAAAAGGATTTCCGTGTGCAAAAAATGAAGAAGATTTAATAATTCAGATTTCATGTGTGTTTTGGCACGCTGGGACGCTTGATGCAACTAGAAATATGCTATTATCTTTAGGGACGTGCTCAGCTGTTGAAAATACTGAAGTTTATGAGTTTCCCAGTGAAATAGACATGCTGCATGGGTTTTTTTCATTAATTAGAGACTTTAATGTTGAAATAATTACTGGTTATAATATTTCTAACTTTGACTTACCCTATCTAATTGATAGAGCTACTCAAATTTATAATATAAAGCTATCTGATTATTCAAGAGTTAAAACAGGGTCTATTTTTCAAGTTCATACGCCAAAAGATACAGGAAAGGGGTTCATGAGATCTGTCTCTAAAATAAAAATTTCAGGAATTATAGCAATTGACATGTACATTGTGTGCAAAGACAAACTCAGTCTGTCTAATTACAAGCTTGATACTGTTGCTAATCACTGCATTAGTGCAAAAAAAGAAGATGTGTCTTACAAAGATATCATGCCTCTTTTTATGTCTGGACCTGAAGGCAGAGCTAAGATAGGACTATACTGTGTAATAGATTCTGTTCTTGTGATGAAACTTTTGAAATTTTTTATGATTCATGTTGAAATTTCTGAGATAGCGAAACTGGCTAAAATCCCCACGAGAAGAGTTCTTACAGATGGGCAACAAATAAGAGTTTTTTCTTGTCTGCTTGCAGCAGCTCGTGCAGAAAACTATATACTGCCTGTGTCAAATGATGTCAATGCGGATGGGTTTCAGGGAGCTACCGTCATAAACCCAATTCCTGGATTTTATAACAATGCTGTATTAGTAGTAGACTTTGCTAGCCTGTATCCTAGTATCATACAAGCTCATAATCTATGCTACTCCACTCTTATACCCCACCATGCTTTACACAACTACCCTCACTTAAAATCTAGTGACTATGAGACTTTTATGCTCAGTTCTGGACCTATACACTTTGTGAAAAAACACATTCAGACATCTCTTCTATCTAGGCTTTTAACTGTGTGGCTTTCTAAGCGAAAGGCTATTAGGCAAAAGCTTGCTGAATGTGAAGACCTAGACACTAAAACTATTCTAGATAAACAGCAACTCGCTATTAAGGTAACCTGTAATGCTGTGTATGGGTTTACAGGAGTTGCGTCAGGCTTGCTGCCATGCATAAGCATTGCAGAGACCGTTACTCTCCAAGGCCGGACGATGCTAGAAAAATCAAAAATATTTATAGAAGCAATGACACCTGATACACTTCAAGAGGATCC

The restriction enzyme sites for EcoRI and BamHI (underlined) were addedto either end of the DNA sequence for easier manipulation.

The terminal repeat probe (GenBank: K03361.1) has the sequence:

(SEQ ID NO: 12) GAATTCGGTCCGGAGCGGTCTCTACAGACGCCCCAGACTCTCAGCTGTCCCCCGGTGCCGGCGCGGCGCCGCTGCCCCCCGCGGCTGGGGAGCTAGGGCCGCTCAAAGCGGGTCCCCTCCCCCGGCCGCCTGGGGATCTGCTAGGCAGCTGCTCTGCAGCCCAGCCTAGGGGGCTTCAGCGGGGCATAGCTCCACAGCGCAAGGGTCCCCGGGCTTCACACTCGGTGGGCAGGCAAGGGACCCTTCCCGCTGACGGCTGCAAACTCTGGCTAGCCGGGGGAACTCTGTGCTGGAGAGATAGGGGCGCGCAAGCCCCCATCACAGGGCTCCGGCTGGCAGGGCTCGCCCTCAGGGCTGCACAGCAGTCTAGCCTAGGGGGCTTCAGCCAGGGCTAGCTCCAAAACCCTCAGGTCCCCAGACTTCAAACTTGGTGGGCACGTAGAGGACCCTTCCCGCTGACTCTCCACGCCGCCTCAGAATTTTAGCACCCGGCGCTGCGGAGCCGGGAGCCAGCAAGCCCCCCGCTGGGGTCTCGGCTGCTGCTGCTCGGGGGCCTGGGGCTGGGGAGGCGGCTGCAGGGGCTGCATGCACTGTGCTTCACGCAGAGGTCGGGGGGGAGCCCAGCTACGCGCCCCCCACGCTGCAGGGCGCTGCGCTGGGCTCTGGGGCTGGGGGGGCTTGAACAGTTGTGGGACCCTTACTCTAGCAGCGCCTCGGCCTAGCCAGGGCTCTGGGGACTGGCTCTAAGCACAGGGGCACAGCGCCCCCGGGCCTGCGGTGGCCTGGGGACACAACAGGAGCTCTGGAATCTCAGCCCAGAGGGGTGCGGGGCTGCTCAATCCCTTCCCCCTCCCTCCGCAGCCGCTCGCTGCTCGCCCTGCCCCCCGAGCTCGCTCTAGCCACGCCCAGGACATTTTTCCAGCTGCCCAGCGCCCACTGCTTGGGGCCCCCCTTCCCCCTCTTTGCCTACCAAGTTATCCCCCGGGGGGAAAATCAGTGGGGGCTGCATAGAGCTCTCCGCAGGCGGCCGCTCGCTCCCCGGGCGTCCGCAGCCTCTCGGGGGGCCTCTGGGGCGCCCGGCGGGAGCCCCCGTGCGGGGCTCCGGTCCCTCTAGTGCACAAGCAGACTCTAGCCCCCTCCCCCAGTACACAGAGCCCAGCAGCCCCCGGCCGCGGCGCCCGTGCAGCGCCCGGCAGCTTGCTTTCGGTTTCTCGCCCCGAGACCCCCGCTGGGCTGCTGGGGGCAGAGCCGCGGGGCCGCAGGCGGGTGCCCTAGAGTCTCAAGCATCTTCTGACTCCGAGTGGAGGGGATCTGTCCCGCTACGGGCTCGCCCTGGGCCGGGGTCTGCAGAGACCGCTCGCGGCGGCCATTTTGTGTGCCACGCATGGCG GTACC

The restriction enzyme sites for EcoRI and KpnI (underlined) were addedto either end of the sequence for easier manipulation.

The viral IL-17 probe (AJ410493.1) has the sequence:

(SEQ ID NO: 13) GGTACCAAACCAACAAGCCAGAACTTAGATTAAACTTTTTTATTTAAAAGAAAAAGATAATCAAGTTTTTGGTTTTTAGCGAAATGTTACTTTTCAAAATTAAGATAGCTCTTAGTCTACATTGTGAACAATAGGAGTAACGCATGTGCAACCTACAGTCACTAGCATCTTCTCTAGCCGAAATGAATTAGGGCAAGGGTTATGCCCTTTGCGCACTACTAGAATCTCTTGTTGGATAGGGACTGAGTTCATGTGGTAGTCTACATTCCCATCAGCATTAACACATCCTAAGTAGCGACACTTTGCTTCCCAAATCACAGAAGGATATCTATCTTGATCTTCATTGCGATAGAGAGTCCAAGGAGACGTAGATCTATTGTAGTAGTCTGAAGCCCTTTTAGAACTAGTATTCCAGTTACGGATGCTCAAAGTAACCATCACAGACCGTGGGAAGCTATTGTTAGCAGCTAAGCATCTTGGGGTTTGTGCGCTGGTTATTTCTGACTTTACTATACAATCTATGCTCAGCAGCAGAAGTAACACAAGTGAAGTCTTTCTAAATGTCATAATTACTTCTTTAAATTATCTATACATGTATAAACAGATAGGCTTGCTATGGTTTACACTAAATGAATGTTTGTTTATATACTTTAGAGTCTTTTATATTGATACAAACTTCTTGCTGCCATATTTTGCTAGTAAAATACAGGGACACCAATACTATACAGAAACATTTTTATTTAAGATTTGCATTTCAGACACTAAGTTATAGCAAACAAGTAATATTGCAATACACAAAGCATTTATTTTAGTATGATAAACACATTCCAACAGTAATTTATGGAGATGA ACTAGTCTTTCTAGA

The restriction enzyme sites for KpnI and XbaI (underlined) were addedto either end of the sequence for easier manipulation.

The viral StpA probe (GenBank: M28071.1) has the sequence:

(SEQ ID NO: 14) TCTAGAGGGCTTGAACAGTTGTGGGACCCTTACTCTAGCAGCGCCTCGGCCTAGCCAGGGCTCTGGGGACTGGCTCTAAGCACAGGGGCACAGCGCCCCCGGGCCTGCGGTGGCCTGGGGACACAACAGGAGCTCTGGAATCTCAGCCCAGAGGGGTGCGGGGCGGTCGCGAGGGTCTAGCGCCTCGAAACCGGCTCGGAGCACAAGCAGACTCTAGCCCCCTCCCCTAGTACACAGAGCCCAGCAGGCAGCTACAGCCGCTCAACGCGAGTCCCTCCCCTTGCTCAAGCTCTTTAGTACACTTTTTGTCTTTTATACAATAGTTTTATTACTGCATAGTATAAGACATTTACTGCAGCACTATGTGATTCACTTTGATTCTTTTACATTTTTTTAAACATAATTACTAGCATTAAACCAATTATGATTAATAGCAAAACAATAATAACTAGCAGCAATAGGATAGTTACAGAACAGTCTGTGCATTTGTCACCTTCTTGCTCGTGTTCACTGTGCAGGCTTCCGACTTCTGCGTAGACATGTTCTTCACTTCCTGCTCCTCCGCAGCCACTGACACGTACTGCTGATAAGCCTACTGGGGTGCTTAAATGTGATGAGCTCCGTGAGCCAGATGGTGTTGGTAAGCCTACTGCTCCCGATAGTGCTGTTGGTCTTCCTGGGCATCCGCTTTCTTGCACTGGGTGGCCAAGCAAGCAGTAGGGATTATAAGGCCCAAAGGGCCCTGCATTTAAAAGCGTTACAGGTAAGTATGGTGTAGGTCCATCATCTCCATCACTTCTTTCATCAGTATTGTGTGGAGGATCTCCGTTGCTTTCATCGTTTTCTTGTGGGTCTCCTTCACCTAGACCTCTTGCCATTTTCTTACACGTCTAAGCTTCAGTTTGTTTAGCTGATTCTTGTAGTGTTGTCTGTCTTGCTAATTCTTATATAGTAGCTTGTTACTTCTTGGAAAGTCCAGCAAGATGGTGTCCTGTTTAACAGCTTGACCACATGTTTTACAGGACTTAAAAATTTAAATTTTAACCTTTTGACAAAGAGCAAAAATGAATAAAAAGCTACAGCTGTATGACTCTTATCTTTTAACATAGTAGCAATGCACTTACGTGTTAACTTATTTTATTATAAGTTGATGCTTGCTATTGTAGTGCTTATAGCAGCTTTTATATCAGCTTTTAGTAGTTATTGCTAGCTTTATCTAGCTTTGCTCTCAATGAGCTGGATCC

The restriction enzyme sites for XbaI and BamHI (underlined) were addedto either end of the sequence for easier manipulation.

The plasmids produced were used to transform Escherichia coli strainTop10, selecting for the ampicillin resistance gene from the pUC57vector using 100 μg/ml ampicillin. The bacteria containing the plasmidswere grown up to isolate plasmid, using the miniprep kit from Promega,following the manufactures instructions.

One μg of each of the plasmids was labeled using the ENZO BioProbe®nick-translation kit with bio-16-dUTP in 50 μl, following themanufacturer's instructions. After labeling, the product wasconcentrated by the addition of 5 μl of 3 M sodium acetate, pH 7 and 130μl of ethanol, followed by freezing for 2 hours at −80° C., thenprecipitating the nucleic acid by centrifugation at 16,100×g for 20minutes. The supernatant was removed by aspiration, and the DNA pelletwas washed using 70% ethanol. The dried pellet was then ready forresuspension and use.

Example 10: Detection of Herpesvirus Saimiri in Clinical Samples UsingBiotinylated Probes

The biotinylated probes described in Example 9 were tested in serialsections of lung tissue samples from IPF patients. When tested in serialsections, the probes for the IL-17 and DNA polymerase sequences(respectively, FIG. 10A, 10C), and the probes for STP and terminalrepeat sequences (data not shown) yielded signal in the sameregenerating epithelial cells in IPF as the LNA probes tested in Example6 (FIG. 6A-6H). No signal was apparent in the negative controls.Co-expression analysis (FIG. 10B, 10D) showed that the same set of cellsthat expressed the viral DNA sequences also co-expressed cyclin D asdetermined by antibody staining. (Compare FIG. 10A with FIG. 10B, andFIG. 10C with FIG. 10D).

Example 11: Effects of Stringency on Hybridization and Detection of HVSProbes in IPF Clinical Specimens

Hybridizations of serial sections of paraffin-embedded IPF samples wascarried out as described previously using either the STP LNA probe asdescribed in Example 1 or a pool of biotin-labeled large probes asdescribed in Example 9. In the case of the LNA probes, washing wasmodified by the addition of a high stringency wash at 50° C. In the caseof the biotin probes, various washing conditions were used as describedin Table 3. For comparison purposes, scores were assigned for signals inthe specimens for each washing condition as also described in Table 3.As controls, clinical specimens from Kaposi's sarcoma and Burkittslymphoma were included as well as both HVS-infected and uninfectedJurkat cells. As evidenced in Table 3, all five IPF specimens scoredpositively with the Herpesvirus saimiri specific probes, although therewere differences in the response to increasing stringency conditionsused for washing the slides. Three of the specimens, 13743, 7480 and71706, showed a difference in hybridization in only one level betweenthe very low stringency and high stringency washes. This result isconsistent with either perfect or a very high level of homology betweenprobe and target. On the other hand, two of the specimens (994326 and205601) showed a difference in two levels, with signal going from 3/0 to1/0 with increasing stringency for 994326 and from 2/0 to 0/0(undetectable) for 20560, indicating that although they did bind to theviral targets, the probes had mismatches with the viral sequences. Itshould also be understood that the results are essentially a qualitativedifference and that there is leeway in the signal scores. Interestingly,neither the Kaposi (HHV8) or Burkitt (EBV) specimens scored positive forprobe binding even under the non-stringent washing conditions. Thecontrol results indicate that the Herpesvirus saimiri virus specificprobes do not bind indiscriminately to other herpesvirus sequences, butrather, that sequences having homology with Herpesvirus saimiri must bepresent for signal generation.

TABLE 3 Compilation of HVS Low vs High Stringency using Biotin or LNAProbe Data LNA Biotin Biotin Biotin (high (very low (low (high Casestringency) stringency*) stringency) stringency) 137431 IPF  3/0** 2/02/0 3/0 99 4326 IPF 3/1 3/0 3/0 1/0 205601 IPF 3/1 2/0 1/0 0/0 7480 IPF3/0 3/0 3/0 2/0 71706 IPF 2/0 2/0 ND 1/0 A (hantavirus 0/0 0/0 0/0 0/0induced IP) 8391 - mediastinal 3/1 1/0 2/0 0/0 lymphoma*** 3406 -mediastinal 3/0 2/0 1/0 1/0 lymphoma 4785 - mediastinal 0/0 0/0 0/0 0/0lymphoma 22926 - mediastinal 0/0 0/0 0/0 0/0 lymphoma 6593 - mediastinal0/0 0/0 0/0 0/0 lymphoma 60218 Castleman's 3/1 2/0 2/0 0/0 disease***32714 Castleman's 3/0 2/0 3/0 0/0 disease Castleman's disease 3/0 3/03/0 0/0 GN Kaposi's sarcoma 0/0 0/0 0/0 0/0 (skin) Burkitt's lymphoma0/0 0/0 0/0 0/0 Jurkat cells NOT 0/0 0/1 0/0 0/0 infected Jurkat cellsInfected 3/0 2/1 2/0 2/0 *high stringency is 0.1XSSC and 2% bovine serumalbumin (BSA) at 50 C. for 5 min, low stringency - 0.1XSSC and 2% bovineserum albumin (BSA) at 4 C. for 5 min, very low stringency = 1.0 XSSCand 2% bovine serum albumin (BSA) at 4 C. for 5 min ** scores reportedas SIGNAL/BACKGROUND with scores of either 0, 1 (weak), 2+ (moderate)and 3+ (intense) *** For the Castleman/Kaposi's/Burkitts/mediastinallymphoma only the Stp and IL-17 probes; for IPF DNA polymerase andTerminal repeat probes also used

Example 12: Effects of Stringency on Hybridization and Detection of HVSProbes with Other Lung Disease Clinical Specimens

Hybridizations and washing conditions as described in Example 11 werealso applied to a series of clinical specimens from lymphomas andCastleman's disease, since these specimens have previously also beenseen to have detectable virus sequences with Herpesvirus saimiri probes(Examples 7 and 8). The results set forth in Table 3 were mixed.Hybridization strength in the lymphoma specimens that were positive forviral sequences showed a difference of only one level between the highstringency and very low stringency conditions. On the other hand, in theCastleman's disease specimens, all three specimens produced very goodsignals (2/0, 3/0 and 3/0) under very low stringency and maintainedtheir signals when stringency was increased to “low stringency”.However, the signal was completely lost when high stringency conditionswere applied using the biotin labeled STP and IL-17 probes described inExample 9. In contrast, the STP LNA probes continued to produce highsignals in all three samples, even after high stringency washing. Theseresults are consistent with the presence in these Castleman's diseasespecimens of a gammavirus that is homologous to Herpesvirus saimiri, butthat has genomic mismatches.

7. ADDITIONAL EMBODIMENTS

This section includes additional embodiments.

-   -   1. A method of diagnosing or prognosticating a viral disease in        a patient comprising a step of detecting the presence of a        virus-specific element from a virus in a clinical sample from        said patient.    -   2. The method of embodiment 1, wherein the virus-specific        element is a nucleic acid.    -   3. The method of embodiment 2, wherein said nucleic acid is        mRNA.    -   4. The method of embodiment 2, wherein said nucleic acid is DNA.    -   5. The method of embodiment 2, wherein said clinical sample is        selected from whole blood, serum, tissue, lavage and        combinations thereof    -   6. The method of embodiment 5, wherein said tissue sample is a        lung biopsy.    -   7. The method of embodiment 6, wherein said tissue sample        comprises a paraffin embedded slide.    -   8. The method of embodiment 2, wherein said detecting step is        carried out by hybridizing the nucleic acid sequence with a        nucleic acid probe comprising a sequence that is complementary        to a virus-specific nucleic acid.    -   9. The method of embodiment 8, where said nucleic acid probe        comprises one or more modified nucleotides.    -   10. The method of embodiment 9, wherein said one or more        modified nucleotides comprises a modified base, a modified        sugar, a modified backbone or combinations thereof    -   11. The method of embodiment 10, wherein the modified base is        selected from 5-methylcytosine, isocytosine, pseudoisocytosine,        5-bromouracil, 5-propynyluracil, 6-aminopurine, 2-aminopurine,        inosine, diaminopurine, 2-chloro-6-aminopurine, xanthine and        hypoxanthine    -   12. The method of embodiment 10, wherein the modified sugar is        selected from a 2′-O-alkyl-ribose sugar, a 2′-amino-deoxyribose        sugar, a 2′-fluoro-deoxyribose sugar, a 2′-fluoro-arabinose        sugar, a 2′-O-methoxyethyl-ribose sugar and an LNA sugar.    -   13. The method of embodiment 10, wherein the backbone        modification is selected from a peptide nucleic acid, a        phosphorothioate linkage, a methylphosphonate, an        alkylphosphonate, a phosphate ester, an alkylphosphonothioate, a        phosphoramidate, a carbamate, a carbonate, a phosphate triester,        an acetamidate, a carboxymethyl ester, a methylphosphorothioate,        a phosphorodithioate, a p-ethoxy linkage, and combinations        thereof    -   14. The method of embodiment 8, wherein said detecting step is        carried out with a nucleic acid isolated from the clinical        sample of said patient.    -   15. The method of embodiment 8, wherein said detecting step is        carried out by fluorescence in-situ hybridization.    -   16. The method of embodiment 2, further comprising a step of        amplifying said nucleic acid prior to said detecting step.    -   17. The method of embodiment 16, wherein said amplifying step is        carried out by PCR or RT-PCR.    -   18. The method of embodiment 16, wherein said amplifying step is        an isothermal process.    -   19. The method of embodiment 18, wherein said isothermal process        is selected from the group consisting of an SDA reaction, a 3 SR        reaction, a NASBA reaction, a TMA reaction, a LAMP reaction, an        HAD reaction, a LAMP reaction, stem-loop amplification, a SMART        reaction, an IMDA reaction, a SPIA reaction, and a cHDA        reaction.    -   20. The method of embodiment 16, wherein said amplifying step is        carried out with a nucleic acid isolated from the clinical        sample of said patient.    -   21. The method of embodiment 16, wherein said detecting step is        carried out in situ with a specimen from said patient.    -   22. The method of embodiment 2, wherein the virus is Herpesvirus        saimiri or a related virus.    -   23. The method of embodiment 2, wherein the viral disease is        idiopathic pulmonary fibrosis, a lymphoproliferative disease or        cancer.    -   24. The method of embodiment 22, wherein the nucleic acid is        selected from a major single-stranded DNA binding protein        (mDNA-BP) gene, a DNA polymerase gene, a DNA packaging, a        terminase gene, a helicase-primase complex gene, a uracil DNA        glycosylase gene, a deoxyuridine triphosphatase (dUTPase) gene,        a DNA polymerase processivity factor gene, a capsid assembly and        DNA maturation protein gene, a TER gene, an STP gene, an IL-17        gene, a Cyclin D gene, a glycoprotein B gene, a Sag gene, a CD59        gene, a Bcl2 gene, a capsid protein gene, an envelope protein        gene, a ribonucleotide reductase gene, a tegument protein gene,        a FLICE interacting protein (FLIP) gene, an IL-8 receptor gene,        a glycoprotein M gene, a FGARAT gene, a thymidine kinase gene, a        phosphotransferase gene, a tyrosine kinase gene, a dihydrofolate        reductase (DHFR) gene, and a thymidylate synthase (TS) gene, a        fragment of any of the foregoing, and combinations thereof    -   25. The method of embodiment 1, wherein the virus-specific        element is a protein or peptide.    -   26. The method of embodiment 25, wherein said protein is an        analog of a human protein, or said peptide is derived from an        analog of a human protein.    -   27. The method of embodiment 25, wherein said clinical sample is        selected from whole blood, serum, tissue, lavage and        combinations thereof    -   28. The method of embodiment 27, wherein said tissue sample is a        lung biopsy.    -   29. The method of embodiment 28, wherein said tissue sample        comprises a paraffin embedded slide.    -   30. The method of embodiment 25, wherein said detecting step is        carried out using an antibody to said virus-specific protein or        peptide.    -   31. The method of embodiment 30, wherein said antibody        recognizes an epitope present in a human protein or peptide and        in a homologous virus-specific protein or peptide.    -   32. The method of embodiment 30, wherein said antibody        recognizes an epitope present in a virus-specific protein or        peptide that is not present in a human protein or peptide.    -   33. The method of embodiment 30, wherein said detecting step is        carried out using an enzyme-linked immuno sorbent assay.    -   34. The method of embodiment 25 wherein said virus-specific        protein is an enzyme.    -   35. The method of embodiment 34 wherein said detecting step is        carried out using an enzyme activity assay.    -   36. The method of embodiment 34, wherein said detecting step is        carried out by detecting a metabolite of the enzyme.    -   37. The method of embodiment 25, wherein the protein or peptide        is from Herpesvirus saimiri or a related virus.    -   38. The method of embodiment 25, wherein the viral disease is        idiopathic pulmonary fibrosis.    -   39. The method of embodiment 37, wherein said protein is        selected from IL-17, thymidylate synthase, dihydrofolate        reductase, cyclin D, STP, Sag, CD59, Bcl2, FGARAT, FLIP, VP23,        glycoprotein B, glycoprotein M, FGARAT, thymidine kinase,        phosphotransferase, tyrosine kinase, uracil DNA glycosylase,        deoxyuridine triphosphatase, major single-stranded DNA binding        protein (mDNA-BP), DNA polymerase, DNA packaging terminase,        helicase-primase complex, uracil DNA glycosylase, deoxyuridine        triphosphatase (dUTPase), DNA polymerase processivity factor,        capsid assembly and DNA maturation protein, a capsid protein, an        envelope protein, ribonucleotide reductase, tegument protein,        IL-8 receptor, or said peptide is derived from any of the        foregoing.    -   40. The method of embodiment 25, which further comprises a step        of detecting a pathogen other than a virus-specific pathogen        that is associated with a viral disease.    -   41. A method of diagnosing or prognosticating a viral disease in        a patient comprising a step of detecting the presence of a human        antibody to a virus-specific element in a clinical sample from        the patient.    -   42. The method of embodiment 41, wherein said clinical sample is        selected from whole blood, serum, tissue, lavage and        combinations thereof    -   43. The method of embodiment 42, wherein said tissue sample is a        lung biopsy.    -   44. The method of embodiment 43, wherein said tissue sample        comprises a paraffin embedded slide.    -   45. The method of embodiment 41, wherein said detecting step is        carried out using an enzyme-linked immune sorbent assay.    -   46. The method of embodiment 41, wherein said human antibody is        to a virus-specific element selected from a capsid protein, an        envelope protein, IL-17, thymidylate synthase, dihydrofolate        reductase, cyclin D, STP, Sag, CD59, Bcl2, FGARAT, FLIP, VP23,        glycoprotein B, glycoprotein M, FGARAT, thymidine kinase,        phosphotransferase, tyrosine kinase, uracil DNA glycosylase,        deoxyuridine triphosphatase, major single-stranded DNA binding        protein (mDNA-BP), DNA polymerase, DNA packaging terminase,        helicase-primase complex, uracil DNA glycosylase, deoxyuridine        triphosphatase (dUTPase), DNA polymerase processivity factor,        capsid assembly and DNA maturation protein, ribonucleotide        reductase, tegument protein, IL-8 receptor and a peptide derived        from any of the foregoing.    -   47. The method of embodiment 41, wherein said virus is        Herpesvirus saimiri or a related virus.    -   48. The method of embodiment 41, wherein said disease is        idiopathic pulmonary fibrosis, a lymphoproliferative disease or        cancer.    -   49. The method of embodiment 1, wherein said virus-specific        element is a viral particle.    -   50. The method of embodiment 49, wherein said clinical sample is        selected from whole blood, serum, tissue, lavage and        combinations thereof    -   51. The method of embodiment 50, wherein said tissue sample is a        lung biopsy.    -   52. The method of embodiment 51, wherein said tissue sample        comprises a paraffin embedded slide.    -   53. The method of embodiment 49, wherein said detecting step is        carried out using an antibody to an envelope protein or a capsid        protein of the virus.    -   54. The method of embodiment 49, wherein the viral particle is        detected by an enzyme-linked immune sorbent assay or flow        cytometry.    -   55. A method of diagnosing or prognosticating a viral disease in        a patient comprising a step of detecting the presence of a cell        infected by the virus in a clinical sample from said patient.    -   56. The method of embodiment 55, wherein said clinical sample is        selected from whole blood, serum, tissue, lavage and        combinations thereof    -   57. The method of embodiment 56, wherein said tissue sample is a        lung biopsy.    -   58. The method of embodiment 57, wherein said tissue sample        comprises a paraffin embedded slide.    -   59. The method of embodiment 49 or embodiment 55, wherein the        virus is Herpesvirus saimiri or a related virus.    -   60. The method of embodiment 49 or 55, wherein the disease is        idiopathic pulmonary fibrosis, a lymphoproliferative disease or        cancer.    -   61. A method of diagnosing or prognosticating a viral disease in        a patient comprising the steps of:    -   (a) measuring expression of a patient nucleic acid or protein in        said patient; and    -   (b) measuring expression of said patient nucleic acid or protein        in a healthy individual, wherein expression measured in step (a)        that is at least two-fold higher than expression measured in        step (b) is indicative of viral disease in said patient.    -   62. The method of embodiment 61, wherein said protein is a viral        analog of a human protein.    -   63. The method of embodiment 62, wherein said protein is        selected from IL-17, cyclin D1 thymidylate synthase, and        dihydrofolate reductase.    -   64. The method of embodiment 61, wherein said nucleic acid is        mRNA that encodes a protein that is a viral analog of a human        protein.    -   65. The method of embodiment 64, wherein said nucleic acid        encodes a protein selected from IL-17, cyclin D1 thymidylate        synthase, and dihydrofolate reductase.    -   66. A method of monitoring progression of a viral disease in a        patient comprising the steps of:    -   (a) measuring a first level of a virus-specific element in a        first clinical sample from the patient;    -   (b) measuring a second level of said virus-specific element in a        second clinical sample from the patient;    -   (c) comparing the first level measured in step (a) and the        second level measured in step (b),    -   wherein the first level measured in step (a) that is less than        the second level measured in step (b) is indicative of disease        progression; and    -   wherein the first level measured in step (a) that is greater        than or equal to the second level measured in step (b) is        indicative of no disease progression or disease remission.    -   67. The method of embodiment 66, wherein step (b) is performed        at least about 1 week after step (a).    -   68. The method of embodiment 66, wherein the virus-specific        element is a virus-specific nucleic acid.    -   69. The method of embodiment 68, wherein said nucleic acid is        DNA.    -   70. The method of embodiment 68, wherein said nucleic acid is        mRNA.    -   71. The method of embodiment 66, wherein said clinical sample is        selected from whole blood, serum, tissue, lavage and        combinations thereof    -   72. The method of embodiment 71, wherein said tissue sample is a        lung biopsy.    -   73. The method of embodiment 72, wherein said tissue sample        comprises a paraffin embedded slide.    -   74. The method of embodiment 66, wherein said virus-specific        element is a nucleic acid sequence selected from a major        single-stranded DNA binding protein (mDNA-BP) gene, a DNA        polymerase gene, a DNA packaging, a terminase gene, a        helicase-primase complex gene, a uracil DNA glycosylase gene, a        deoxyuridine triphosphatase (dUTPase) gene, a DNA polymerase        processivity factor gene, a capsid assembly and DNA maturation        protein gene, a TER gene, an STP gene, a repetitive DNA        sequence, an IL-17 gene, a Cyclin D gene, a glycoprotein B gene,        a Sag gene, a CD59 gene, a Bcl2 gene, a capsid protein gene, an        envelope protein gene, a ribonucleotide reductase gene, a        tegument protein gene, a FLICE interacting protein (FLIP) gene,        an IL-8 receptor gene, a glycoprotein M gene, a FGARAT gene, a        thymidine kinase gene, a phosphotransferase gene, a tyrosine        kinase gene, a dihydrofolate reductase (DHFR) gene, and a        thymidylate synthase gene, a fragment of any of the foregoing,        and combinations thereof    -   75. The method of embodiment 66, wherein said virus is        Herpesvirus saimiri or a related virus.    -   76. The method of embodiment 66, wherein the disease is        idiopathic pulmonary fibrosis, a lymphoproliferative disease or        cancer.    -   77. The method of embodiment 66, wherein said virus-specific        element is a protein or peptide.    -   78. The method of embodiment 77, wherein said protein is an        analog of a human protein, or said peptide is derived from an        analog of a human protein.    -   79. The method of embodiment 77, wherein said clinical sample is        selected from whole blood, serum, tissue, lavage and        combinations thereof 80. The method of embodiment 79, wherein        said tissue sample is a lung biopsy.    -   81. The method of embodiment 80, wherein said tissue sample        comprises a paraffin embedded slide.    -   82. The method of embodiment 77, wherein said detecting step is        carried out using an antibody to said virus-specific protein or        peptide.    -   83. The method of embodiment 82, wherein said antibody        recognizes an epitope present in a human protein or peptide and        in a homologous virus-specific protein or peptide.    -   84. The method of embodiment 82, wherein said antibody        recognizes an epitope present in a virus-specific protein or        peptide that is not present in a human protein or peptide.    -   85. The method of embodiment 82, wherein said detecting step is        carried out using an enzyme-linked immuno sorbent assay.    -   86. The method of embodiment 77 wherein said virus-specific        protein is an enzyme.    -   87. The method of embodiment 86 wherein said detecting step is        carried out using an enzyme activity assay.    -   88. The method of embodiment 86, wherein said detecting step is        carried out by detecting a metabolite of the enzyme.    -   89. The method of embodiment 77, wherein the virus is        Herpesvirus saimiri or a related virus.    -   90. The method of embodiment 77, wherein the disease is        idiopathic pulmonary fibrosis, a lymphoproliferative disease or        cancer.    -   91. The method of embodiment 89, wherein said protein is        selected from IL-17, thymidylate synthase, dihydrofolate        reductase, cyclin D, STP, Sag, CD59, Bcl2, FGARAT, FLIP, VP23,        glycoprotein B, glycoprotein M, FGARAT, thymidine kinase,        phosphotransferase, tyrosine kinase, uracil DNA glycosylase,        deoxyuridine triphosphatase, major single-stranded DNA binding        protein (mDNA-BP), DNA polymerase, DNA packaging terminase,        helicase-primase complex, uracil DNA glycosylase, deoxyuridine        triphosphatase (dUTPase), DNA polymerase processivity factor,        capsid assembly and DNA maturation protein, a capsid protein, an        envelope protein, ribonucleotide reductase, tegument protein,        IL-8 receptor, or said peptide is derived from any of the        foregoing.    -   92. A method of monitoring progression of a viral disease in a        patient comprising the steps of:    -   (a) measuring a first level of a patient antibody to a        virus-specific element in a first clinical sample from the        patient;    -   (b) measuring a second level of the patient antibody to a        virus-specific element in a second clinical sample from the        patient;    -   (c) comparing the first level measured in step (a) and the        second level measured in step (b),    -   wherein the first level measured in step (a) that is less than        the second level measured in step (b) is indicative of disease        progression; and    -   wherein the first level measured in step (a) that is greater        than or equal to the second level measured in step (b) is        indicative of no disease progression or disease remission.    -   93. The method of embodiment 92, wherein step (b) is performed        at least about 1 week after step (a).    -   94. The method of embodiment 92, wherein said clinical sample is        selected from whole blood, serum, tissue, lavage and        combinations thereof    -   95. The method of embodiment 94, wherein said tissue sample is a        lung biopsy.    -   96. The method of embodiment 95, wherein said tissue sample        comprises a paraffin embedded slide.    -   97. The method of embodiment 96, wherein said measuring steps        are carried out using an enzyme-linked immune sorbent assay.    -   98. The method of embodiment 92, wherein said human antibody is        to a virus-specific element selected from a capsid protein, an        envelope protein, IL-17, thymidylate synthase, dihydrofolate        reductase, cyclin D, STP, Sag, CD59, Bcl2, FGARAT, FLIP, VP23,        glycoprotein B, glycoprotein M, FGARAT, thymidine kinase,        phosphotransferase, tyrosine kinase, uracil DNA glycosylase,        deoxyuridine triphosphatase, major single-stranded DNA binding        protein (mDNA-BP), DNA polymerase, DNA packaging terminase,        helicase-primase complex, uracil DNA glycosylase, deoxyuridine        triphosphatase (dUTPase), DNA polymerase processivity factor,        capsid assembly and DNA maturation protein, ribonucleotide        reductase, tegument protein, IL-8 receptor and a peptide derived        from any of the foregoing.    -   99. The method of embodiment 92, wherein said virus is        Herpesvirus saimiri or a related virus.    -   100. The method of embodiment 92, wherein the disease is        idiopathic pulmonary fibrosis, a lymphoproliferative disease or        cancer.    -   101. A method of monitoring the efficacy of a therapy for        treatment of a viral disease comprising the steps of:    -   (a) measuring a first level of a virus-specific element in a        first clinical sample from an untreated patient;    -   (b) measuring a second level of said virus-specific element in a        second clinical sample from said patient after treatment; and    -   (c) comparing the first level measured in step (a) and the        second level measured in step (b),    -   wherein the first level measured in step (a) that is greater        than or equal to the second level measured in step (b) is        indicative of the efficacy of the therapy.    -   102. The method of embodiment 101, wherein step (b) is performed        at least about 1 week after the therapy is administered.    -   103. The method of embodiment 101, wherein said clinical sample        is selected from whole blood, serum, tissue, lavage and        combinations thereof    -   104. The method of embodiment 103, wherein said tissue sample is        a lung biopsy.    -   105. The method of embodiment 104, wherein said tissue sample        comprises a paraffin embedded slide.    -   106. The method of embodiment 101, wherein said virus-specific        element is a nucleic acid.    -   107. The method of embodiment 106, wherein said nucleic acid is        mRNA.    -   108. The method of embodiment 106, wherein said nucleic acid is        DNA.    -   109. The method of embodiment 106, wherein the nucleic acid is        selected from a major single-stranded DNA binding protein        (mDNA-BP) gene, a DNA polymerase gene, a DNA packaging, a        terminase gene, a helicase-primase complex gene, a uracil DNA        glycosylase gene, a deoxyuridine triphosphatase (dUTPase) gene,        a DNA polymerase processivity factor gene, a capsid assembly and        DNA maturation protein gene, a TER gene, an STP gene, an IL-17        gene, a Cyclin D gene, a glycoprotein B gene, a Sag gene, a CD59        gene, a Bcl2 gene, a capsid protein gene, an envelope protein        gene, a ribonucleotide reductase gene, a tegument protein gene,        a FLICE interacting protein (FLIP) gene, an IL-8 receptor gene,        a glycoprotein M gene, a FGARAT gene, a thymidine kinase gene, a        phosphotransferase gene, a tyrosine kinase gene, a dihydrofolate        reductase (DHFR) gene, and a thymidylate synthase gene, a        fragment of any of the foregoing, and combinations thereof    -   110. The method of embodiment 101, wherein the virus-specific        element is a protein or peptide.    -   111. The method of embodiment 110, wherein the protein is an        enzyme.    -   112. The method of embodiment 110, wherein the protein is        selected from a capsid protein, an envelope protein, IL-17,        thymidylate synthase, dihydrofolate reductase, cyclin D, STP,        Sag, CD59, Bcl2, FGARAT, FLIP, VP23, glycoprotein B,        glycoprotein M, FGARAT, thymidine kinase, phosphotransferase,        tyrosine kinase, uracil DNA glycosylase, deoxyuridine        triphosphatase, major single-stranded DNA binding protein        (mDNA-BP), DNA polymerase, DNA packaging terminase,        helicase-primase complex, uracil DNA glycosylase, deoxyuridine        triphosphatase (dUTPase), DNA polymerase processivity factor,        capsid assembly and DNA maturation protein, ribonucleotide        reductase, tegument protein, IL-8 receptor and a peptide derived        from any of the foregoing.    -   113. The method of embodiment 111, wherein the protein is        selected from thymidylate synthase, dihydrofolate reductase,        thymidine kinase, phosphotransferase, tyrosine kinase, uracil        DNA glycosylase, deoxyuridine triphosphatase, DNA polymerase,        DNA packaging terminase, helicase-primase complex, uracil DNA        glycosylase, deoxyuridine triphosphatase (dUTPase), DNA        polymerase processivity factor, and ribonucleotide reductase.    -   114. The method of embodiment 111, wherein the virus-specific        element is a virus-specific metabolite of said enzyme.    -   115. The method of embodiment 101, wherein said virus is        Herpesvirus saimiri or a related virus.    -   116. The method of embodiment 101, wherein said viral disease is        idiopathic pulmonary fibrosis, a lymphoproliferative disease or        cancer.    -   117. A method of monitoring the efficacy of a therapy for        treatment of a viral disease in a patient comprising the steps        of:    -   (a) measuring a first level of a patient antibody to a        virus-specific element in a first clinical sample from the        patient;    -   (b) measuring a second level of the patient antibody to the        virus-specific element in a second clinical sample from the        patient;    -   (c) comparing the first level measured in step (a) and the        second level measured in step (b),    -   wherein the first level measured in step (a) that is greater        than or equal to the second level measured in step (b) is        indicative of the efficacy of the therapy.    -   118. The method of embodiment 117, wherein step (b) is performed        at least about 1 week after step (a).    -   119. The method of embodiment 117, wherein said clinical sample        is selected from whole blood, serum, tissue, lavage and        combinations thereof 120. The method of embodiment 119, wherein        said tissue sample is a lung biopsy.    -   121. The method of embodiment 120, wherein said tissue sample        comprises a paraffin embedded slide.    -   122. The method of embodiment 117, wherein said measuring steps        are carried out using an enzyme-linked immune sorbent assay.    -   123. The method of embodiment 117, wherein said human antibody        is to a virus-specific element selected from a capsid protein,        an envelope protein, IL-17, thymidylate synthase, dihydrofolate        reductase, cyclin D, STP, Sag, CD59, Bcl2, FGARAT, FLIP, VP23,        glycoprotein B, glycoprotein M, FGARAT, thymidine kinase,        phosphotransferase, tyrosine kinase, uracil DNA glycosylase,        deoxyuridine triphosphatase, major single-stranded DNA binding        protein (mDNA-BP), DNA polymerase, DNA packaging terminase,        helicase-primase complex, uracil DNA glycosylase, deoxyuridine        triphosphatase (dUTPase), DNA polymerase processivity factor,        capsid assembly and DNA maturation protein, ribonucleotide        reductase, tegument protein, IL-8 receptor and a peptide derived        from any of the foregoing.    -   124. The method of embodiment 117, wherein said virus is        Herpesvirus saimiri or a related virus.    -   125. The method of embodiment 117, wherein said disease is        idiopathic pulmonary fibrosis, a lymphoproliferative disease or        cancer.    -   126. A method of identifying in vitro a therapeutic agent for        the treatment of a viral disease, comprising the steps of    -   (a) exposing a virus culture to said agent;    -   (b) measuring the replication of said virus culture; and    -   (c) comparing said replication measured in step (b) with the        replication of a virus culture that has not been exposed to the        agent,    -   wherein replication measured in step (b) that is lower than        replication of a virus culture that has not been exposed to the        agent identifies a therapeutic agent for the treatment of said        viral disease.    -   127. The method of embodiment 126, wherein the virus is cultured        in a permissive cell line.    -   128. The method of embodiment 126, wherein the virus is cultured        in a semi-permissive cell line.    -   129. The method of embodiment 126, wherein the virus is cultured        in vitro in human T-lymphocytes.    -   130. The method of embodiment 126, wherein viral replication is        measured by measuring an amount of viral particles.    -   131. The method of embodiment 126, wherein viral replication is        measured by measuring an amount of infected host cells.    -   132. The method of embodiment 126, wherein replication is        measured by measurement of a virus-specific element.    -   133. The method of embodiment 132, wherein said virus-specific        element is a nucleic acid.    -   134. The method of embodiment 133, which includes a step of        amplifying said nucleic acid before said measuring step (b).    -   135. The method of embodiment 133 wherein the nucleic acid is        DNA.    -   136. The method of embodiment 133, wherein the nucleic acid is        mRNA.    -   137. The method of embodiment 132, wherein said virus-specific        element is a protein or peptide.    -   138. The method of embodiment 137, wherein the protein is an        enzyme.    -   139. The method of embodiment 138, wherein said virus-specific        element is a metabolite of said enzyme.    -   140. The method of embodiment 137, wherein the protein is        selected from IL-17, thymidylate synthase, dihydrofolate        reductase, cyclin D, STP, Sag, CD59, Bcl2, FGARAT, FLIP, VP23,        glycoprotein B, glycoprotein M, FGARAT, thymidine kinase,        phosphotransferase, tyrosine kinase, uracil DNA glycosylase,        deoxyuridine triphosphatase, major single-stranded DNA binding        protein (mDNA-BP), DNA polymerase, DNA packaging terminase,        helicase-primase complex, uracil DNA glycosylase, deoxyuridine        triphosphatase (dUTPase), DNA polymerase processivity factor,        capsid assembly and DNA maturation protein, a capsid protein, an        envelope protein, ribonucleotide reductase, tegument protein,        IL-8 receptor, or said peptide is derived from any of the        foregoing.    -   141. The method of embodiment 138, wherein the enzyme is        selected from thymidylate synthase, dihydrofolate reductase,        thymidine kinase, phosphotransferase, tyrosine kinase, uracil        DNA glycosylase, deoxyuridine triphosphatase, DNA polymerase,        DNA packaging terminase, helicase-primase complex, uracil DNA        glycosylase, deoxyuridine triphosphatase (dUTPase), DNA        polymerase processivity factor, and ribonucleotide reductase.    -   142. The method of embodiment 126, wherein the virus is        Herpesvirus saimiri or a related virus.    -   143. The method of embodiment 126, wherein the viral disease is        idiopathic pulmonary fibrosis, a lymphoproliferative disease or        cancer.    -   144. A method of identifying in vitro a therapeutic agent for        the treatment of a viral disease, comprising the steps of    -   (a) exposing a virus culture to an agent;    -   (b) measuring the activity of a viral protein in said culture;        and    -   (c) comparing said activity measured in step (b) with the        activity of the viral protein in a virus culture that has not        been exposed to the agent,    -   wherein activity of the viral protein measured in step (b) that        is lower than the activity of the viral protein in the virus        culture that has not been exposed to the agent identifies a        therapeutic agent for the treatment of said viral disease.    -   145. The method of embodiment 144, wherein the viral protein is        an enzyme.    -   146. The method of embodiment 145, wherein the activity of the        enzyme is measured by measuring an amount of a metabolite of        said enzyme.    -   147. The method of embodiment 145, wherein the viral protein is        selected from thymidylate synthase, dihydrofolate reductase,        thymidine kinase, phosphotransferase, tyrosine kinase, uracil        DNA glycosylase, deoxyuridine triphosphatase, DNA polymerase,        DNA packaging terminase, helicase-primase complex, uracil DNA        glycosylase, deoxyuridine triphosphatase (dUTPase), DNA        polymerase processivity factor, and ribonucleotide reductase.    -   148. The method of embodiment 144, wherein the viral protein is        a cytokine.    -   149. The method of embodiment 148, wherein the activity of the        protein is measured by measuring the activity of a reporter gene        that is regulated by said cytokine.    -   150. A method of treating a patient suffering from a viral        disease comprising administering to the patient an effective        amount of an agent identified by the method of embodiment 124 or        embodiment 142.    -   151. The method of embodiment 150, which further comprises        administering an effective amount of an anti-viral agent.    -   152. The method of embodiment 151, wherein the anti-viral agent        is selected from the group consisting of acyclovir, vidarabine,        idoxuridine, brivudine, cytarabine, foscarnet, docosanol,        formivirsen, tromantidine, imiquimod, podophyllotoxin,        cidofovir, interferon alpha-2b, peginterferon alpha-2a,        ribavirin, moroxydine, valacyclovir, trifluridine,        bromovinyldeoxyuridine, and combinations thereof    -   153. The method of embodiment 150, which further comprises        administering an effective amount of IL-10 or an agonist of        IL-10.    -   154. The method of embodiment 153, wherein the agonist of IL-10        is selected from the group consisting of isoproterenol, IT 9302        and combinations thereof    -   155. A method of treating a patient suffering from a viral        disease comprising administering to the patient an effective        amount of an agent that inhibits replication of a virus.    -   156. The method of embodiment 155, wherein said agent is        selected from a nucleotide analog, a viral polymerase inhibitor,        an inhibitor of a viral protein essential for viral DNA        maturation, an inhibitor of episomal persistence of a genome of        the virus, and combinations thereof    -   157. A method of treating a patient suffering from a viral        disease comprising administering to the patient an effective        amount of an agent that down-regulates expression of a        virus-specific protein.    -   158. The method of embodiment 157, wherein said agent is        selected from antisense DNA, antisense mRNA, RNAi, a ribosome,        and combinations thereof    -   159. A method of treating a patient suffering from a viral        disease, comprising administering to said patient an effective        amount of an antagonist of a viral protein or a neutralizing        agent that blocks activity of a viral protein.    -   160. The method of embodiment 159, wherein the antagonist is an        antibody to virus-specific IL-17.    -   161. The method of embodiment 160, wherein the antibody is a        monoclonal antibody.    -   162. The method of embodiment 160, wherein the antibody is a        polyclonal antibody.    -   163. The method of embodiment 160, wherein the antibody is a        human antibody.    -   164. The method of embodiment 160, wherein the antibody is        humanized.    -   165. The method of embodiment 160, wherein the antibody binds to        virus-specific IL-17, but not to human IL-17.    -   166. The method of embodiment 165, wherein the antibody is        specific for IL-17A.    -   167. The method of embodiment 159, wherein the neutralizing        agent is an antibody to an IL-17 receptor (IL17R).    -   168. The method of embodiment 167, wherein the antibody is        specific for one or more of IL17RA, IL17RB, and IL17RC.    -   169. The method of embodiment 167, wherein the antibody is a        monoclonal antibody.    -   170. The method of embodiment 167, wherein the antibody is a        polyclonal antibody.    -   171. The method of embodiment 167, wherein the antibody is a        human antibody.    -   172. The method of embodiment 167, wherein the antibody is        humanized.    -   173. The method of embodiment 160, which further comprises        administering an effective amount of IL-10 or an agonist of        IL-10.    -   174. The method of embodiment 173, wherein the agonist of IL-10        is selected from the group consisting of isoproterenol, IT 9302        and combinations thereof 175. The method of embodiment 159,        wherein the neutralizing agent is an antagonist of TGF-β.    -   176. The method of embodiment 173, wherein the antagonist is an        antibody to TGF-β.    -   177. The method of embodiment 174, wherein the antibody is a        monoclonal antibody.    -   178. The method of embodiment 174, wherein the antibody is a        polyclonal antibody.    -   179. The method of embodiment 174, wherein the antibody is a        human antibody.    -   180. The method of embodiment 174, wherein the antibody is        humanized.    -   181. The method of embodiment 157, wherein the neutralizing        agent is an antibody to a TGF-β receptor.    -   182. The method of embodiment 175, which further comprises        administering an effective amount of IL-10 or an agonist of        IL-10.    -   183. The method of embodiment 182, wherein the agonist of IL-10        is selected from the group consisting of isoproterenol, IT 9302        and combinations thereof    -   184. The method of embodiment 159, wherein the neutralizing        agent is an antagonist of human IL-23.    -   185. The method of embodiment 184, wherein the antagonist of        IL-23 is an antibody.    -   186. The method of embodiment 185, wherein the antibody is a        monoclonal antibody.    -   187. The method of embodiment 185, wherein the antibody is a        polyclonal antibody.    -   188. The method of embodiment 185, wherein the antibody is a        human antibody.    -   189. The method of embodiment 185, wherein the antibody is        humanized.    -   190. The method of embodiment 185, wherein the neutralizing        agent of human IL-23 is an antibody to an IL-23 receptor.    -   191. The method of embodiment 190, wherein the antibody is a        monoclonal antibody.    -   192. The method of embodiment 190, wherein the antibody is a        polyclonal antibody.    -   193. The method of embodiment 190, wherein the antibody is a        human antibody.    -   194. The method of embodiment 190, wherein the antibody is        humanized.    -   195. The method of embodiment 184, which further comprises        administering an effective amount of IL-10 or an agonist of        IL-10.    -   196. The method of embodiment 195, wherein the agonist of IL-10        is selected from the group consisting of isoproterenol, IT 9302        and combinations thereof    -   197. The method of embodiment 159, wherein the neutralizing        agent is an antagonist of IL-1β.    -   198. The method of embodiment 197, wherein the antagonist is an        antibody to IL-1β.    -   199. The method of embodiment 198, wherein the antibody is a        monoclonal antibody.    -   200. The method of embodiment 199, wherein the antibody is        Canakinumab.    -   201. The method of embodiment 198, wherein the antibody is a        polyclonal antibody.    -   202. The method of embodiment 198, wherein the antibody is a        human antibody.    -   203. The method of embodiment 198, wherein the antibody is        humanized.    -   204. The method of embodiment 159, wherein the neutralizing        agent is a soluble IL-17R extra-cellular domain.    -   205. The method of embodiment 204, wherein the soluble IL-17R        extra-cellular domain is an IL-17RA extra-cellular domain.    -   206. The method of embodiment 204, wherein the soluble IL-17R        extra-cellular domain is an IL-17RB extra-cellular domain.    -   207. The method of embodiment 204, wherein the soluble IL-17R        extra-cellular domain is an IL-17RC extra-cellular domain.    -   208. The method of embodiment 159, wherein the neutralizing        agent is a soluble IL-R8 extra-cellular domain.    -   209. A method of treating a patient suffering from a viral        disease, comprising administering to said patient an effective        amount of an agent that inhibits virus entry into a host cell.    -   210. The method of embodiment 209, wherein said agent is        selected from an small molecule or peptide that binds to a virus        surface glycoprotein and blocks binding of the virus to a host        cell receptor, a soluble extra-cellular domain of a        virus-specific glycoprotein, an antibody that binds to a        virus-specific glycoprotein and an antibody that binds to a host        cell receptor.    -   211. A method of treating a patient suffering from a viral        disease, comprising administering to said patient an effective        amount of an agent that inhibits an enzyme of a virus.    -   212. The method of embodiment 211, wherein the agent is selected        from a reversible enzyme inhibitor, an irreversible enzyme        inhibitor, a competitive enzyme inhibitor, an uncompetitive        enzyme inhibitor, a mixed inhibition enzyme inhibitor, and a        non-competitive inhibitor.    -   213. A vaccine composition against a viral infection comprising        an effective immunizing amount of an antigen selected from the        group consisting a virus, a viral membrane associated antigen, a        viral latency-associated nuclear antigen, a viral cytoplasmic        late antigen, a viral nuclear early antigen, a viral antigenic        protein or peptide, and combinations thereof, and a        pharmaceutically acceptable excipient.    -   214. The vaccine of embodiment 213, wherein the virus is a live        attenuated whole virus.    -   215. The vaccine of embodiment 213, wherein the virus is an        inactivated virus.    -   216. The vaccine of embodiment 213, wherein the viral membrane        associated antigen is in a plasma membrane vesicle.    -   217. The vaccine of embodiment 214, wherein the live attenuated        whole virus comprises an inactivating mutation in the genome of        said virus.    -   218. The vaccine of embodiment 217, wherein the inactivating        mutation comprises a deletion, substitution or insertion in an        endogenous promoter region of an intermediate-early gene.    -   219. The vaccine of embodiment 214, wherein said virus is        incapable of establishing latent infection.    -   220. The vaccine of embodiment 213, wherein said        pharmaceutically acceptable excipient is selected from the group        consisting of an adjuvant, a preservative, a diluent, a        stabilizer, a buffer, a solvent, an inactivating agent, a viral        inactivator, an antimicrobial, a tonicity agent, a surfactant, a        thickening agent and combinations thereof    -   221. The vaccine of embodiment 213, wherein the antigenic        protein or peptide is a capsid protein, an envelope protein, a        peptide derived from either a capsid protein or an envelope        protein, and combinations thereof    -   222. The vaccine of embodiment 220, wherein the adjuvant is        selected from the group consisting of an aluminum salt, an        organic adjuvant, an oil-in-water adjuvant, a virosome, and an        immunological adjuvant.    -   223. The vaccine of embodiment 221, wherein the adjuvant is        selected from the group consisting of aluminum phosphate,        aluminum hydroxide, aluminum phosphate, squalene, an extract of        Quillaja saponaria, MF59, QS21, Malp2, incomplete Freund's        adjuvant, complete Freund's adjuvant, Alhydrogel®, 3        De-O-acylated monophosphoryl lipid A (3D-MPL), Matrix-M™ and        combinations thereof    -   224. The method of embodiment 213, wherein said virus is        Herpesvirus saimiri and said viral infection is idiopathic        pulmonary fibrosis, a lymphoproliferative disease or cancer.    -   225. A kit for diagnosing a viral disease in a patient        comprising one or more probes complementary to a nucleic acid        sequence of a virus.    -   226. The kit of embodiment 125, wherein said one or more probes        comprises one or more affinity-enhancing nucleotides.    -   227. The kit of embodiment 225, wherein said one or more probes        comprises a locked nucleic acid.    -   228. The kit of embodiment 225, wherein said one or more probes        comprises a peptide nucleic acid.    -   229. The kit of embodiment 225, which further comprises a        reagent for amplifying the viral nucleic acid.    -   230. A kit for diagnosing a viral disease in a patient        comprising an immunological reagent for detection and/or        quantification of a virus-specific protein, peptide or        metabolite.    -   231. The kit of embodiment 230, wherein the immunological        reagent is an antibody to a virus-specific protein, peptide or        metabolite.    -   232. A kit for diagnosing a viral disease in a patient        comprising an immunological reagent for detection and/or        quantification of a human antibody to a virus-specific element.    -   233. The kit of embodiment 232, wherein the virus-specific        element is a protein, peptide or metabolite.    -   234. The kit of embodiment 232, wherein the virus-specific        element is a viral particle.    -   235. The kit of embodiment 232, wherein immunological reagent is        an antibody to a virus capsid protein or a virus envelope        protein.    -   236. The kit of embodiment 232, wherein the virus-specific        element is a viral marker on the surface of an infected host        cell.    -   237. The method of any one of embodiments 225, 230 and 232,        which further comprises one or more of (i) a cell line for        culturing a virus; (ii) a cell growth medium; and (iii) a        buffer.    -   238. The method of embodiment 237, wherein the cell line is        selected from a permissive cell line and a semi-permissive cell        line.    -   239. A kit for diagnosing a viral disease in a patient        comprising:    -   (a) a reagent for carrying out amplification of a nucleic acid        sequence;    -   (b) a primer comprising a sequence complementary to a sequence        in one strand of the viral genome; and    -   (c) a primer comprising a sequence identical to a sequence in        said strand of the viral genome,    -   wherein said primers are capable of amplifying a nucleic acid of        said virus when said nucleic acid is present.    -   240. The kit of embodiment 239, wherein said reagent is for        carrying out PCR.    -   241. The kit of embodiment 240 wherein said reagent is for        detection in real time.    -   242. The kit of 239, wherein said reagent is selected from a        Taqman probe, a molecular beacon, a yin-yang probe set, an        energy transfer labeled primer, an energy transfer labeled        probe, an energy transfer labeled nucleotide, an intercalating        dye and a combination thereof    -   243. The kit of embodiment 239 wherein said reagent is for        carrying out in situ PCR.    -   244. The kit of embodiment 237 wherein said reagent is        appropriate for carrying out an isothermal amplification        reaction.    -   245. The kit of embodiment 244, wherein said amplification        reaction is selected from SDA reaction, a 3SR reaction, a NASBA        reaction, a TMA reaction, a LAMP reaction, an HAD reaction, a        LAMP reaction, stem-loop amplification, a SMART reaction, an        IMDA reaction, a SPIA reaction, and a cHDA reaction.    -   246. The kit of any one of embodiments 225, 230 and 232 and 239,        wherein the virus is Herpesvirus saimiri and the disease is        idiopathic pulmonary fibrosis, a lymphoproliferative disease or        cancer.    -   247. A method of diagnosing or prognosticating a viral disease        in a patient comprising a step of detecting the presence of a        virus-specific element from a virus in a clinical sample from        said patient.    -   248. The method of embodiment 246, wherein the virus-specific        element is a nucleic acid selected from mRNA and DNA.    -   249. The method of embodiment 248, wherein said clinical sample        is selected from whole blood, serum, tissue, lavage and        combinations thereof    -   250. The method of embodiment 248, further comprising a step of        amplifying said nucleic acid prior to said detecting step by PCR        or RT-PCR.    -   251. The method of embodiment 248, wherein the virus is        Herpesvirus saimiri or a related virus.    -   252. The method of embodiment 248, wherein the viral disease is        idiopathic pulmonary fibrosis.    -   253. The method of embodiment 247, wherein the virus-specific        element is a protein or peptide.    -   254. The method of embodiment 253, wherein said detecting step        is carried out using an antibody to said virus-specific protein        or peptide.    -   255. A method of identifying in vitro a therapeutic agent for        the treatment of a viral disease, comprising the steps of    -   (a) exposing a virus culture to said agent;    -   (b) measuring the propagation of said virus culture; and    -   (c) comparing said propagation measured in step (b) with the        propagation of a virus culture that has not been exposed to the        agent,    -   wherein propagation measured in step (b) that is lower than        propagation of a virus culture that has not been exposed to the        agent identifies a therapeutic agent for the treatment of said        viral disease.    -   256. The method of embodiment 255, wherein the virus is cultured        in a permissive cell line, a semi-permissive cell line or human        T-lymphocytes.    -   257. The method of embodiment 255, wherein viral propagation is        measured by measuring an amount of viral particles.    -   258. The method of embodiment 255, wherein viral propagation is        measured by measuring an amount of infected host cells.    -   259. A method of treating a patient suffering from a viral        disease comprising administering to the patient an effective        amount of an agent that inhibits replication of a virus, an        effective amount of an agent that down-regulates expression of a        virus-specific protein, an antagonist of a viral protein or a        neutralizing agent that blocks activity of a viral protein.    -   260. The method of embodiment 259, wherein the antagonist is an        antibody to virus-specific IL-17.    -   261. A kit for diagnosing a viral disease in a patient        comprising:    -   (a) a reagent for carrying out amplification of a nucleic acid        sequence;    -   (b) a primer comprising a sequence complementary to a sequence        in one strand of the viral genome; and    -   (c) a primer comprising a sequence identical to a sequence in        said strand of the viral genome,    -   wherein said primers are capable of amplifying a nucleic acid of        said virus when said nucleic acid is present.    -   262. The kit of embodiment 261, wherein said reagent is for        carrying out PCR.    -   263. The kit of embodiment 262 wherein said reagent is for        detection in real time.    -   264. The kit of embodiment 262, wherein said reagent is selected        from a Taqman probe, a molecular beacon, a yin-yang probe set,        an energy transfer labeled primer, an energy transfer labeled        probe, an energy transfer labeled nucleotide, an intercalating        dye and a combination thereof    -   265. The kit of embodiment 262, wherein the virus is Herpesvirus        saimiri and the disease is idiopathic pulmonary fibrosis.    -   266. A method of detecting the presence of viral target        sequences in a human clinical sample comprising the steps of:    -   a. providing        -   i. a human clinical sample suspected of having a viral            infection,        -   ii. a labeled nucleic acid probe comprising one or more            sequences derived from Herpesvirus saimiri,    -   b. contacting said clinical sample (i) with said labeled nucleic        acid probe (ii),    -   c. allowing hybridization to take place between said labeled        nucleic acid probe (ii) and nucleic acids with viral sequences        in said clinical sample (i) if present, and    -   d. detecting hybridization of said nucleic acid probe (ii) to        nucleic acids in said clinical sample (i).    -   267. The method of embodiment 266, wherein said viral target        sequences comprises mRNA.    -   268. The method of embodiment 266, wherein said viral target        sequences comprises DNA.    -   269. The method of embodiment 266, wherein said nucleic acid        probe is labeled with a radioactive label, a fluorescent label,        a chemiluminescent label, a hapten label, an enzymatic label, a        labeled binding partner label, a chromogenic label, or an energy        transfer pair.    -   270. The method of embodiment 269, wherein said labeled binding        partner is biotin, avidin or streptavidin.    -   271. The method of embodiment 266, wherein said human clinical        sample is selected from blood, tissue, lavage, and combinations        thereof.    -   272. The method of embodiment 271, wherein said tissue sample is        a lung biopsy.    -   273. The method of embodiment 271, wherein said clinical sample        comprises a paraffin embedded slide.    -   274. The method of embodiment 266, wherein said method of        detection comprises in situ hybridization or flow cytometry.    -   275. The method of embodiment 266, wherein said providing step        comprises isolation of nucleic acids from said clinical sample.    -   276. The method of embodiment 275, further comprising a nucleic        acid amplification step before or concurrently with step b.    -   277. The method of embodiment 276, wherein said amplification        step is carried out by an Eberwine amplification, a polymerase        chain reaction (PCR) amplification, an AmpiProbe® amplification,        a real time polymerase chain reaction (RT-PCR) amplification, a        degenerate oligonucletotide primer PCR (DOP-PCR) amplification,        a multiple displacement amplification, a self-sustained sequence        reaction (3SR) amplification, a nucleic acid based transcription        assay (NASBA) amplification, a transcription mediated        amplification (TMA), a strand displacement amplification (SDA),        a helicase-dependent amplification (HDA), a loop-mediated        isothermal amplification (LAMP), a stem-loop amplification, a        signal mediated amplification of RNA technology (SMART), an        isothermal multiple displacement amplification (IMDA), a single        primer isothermal amplification (SPIA), or a circular        helicase-dependent amplification (cHDA).    -   278. The method of embodiment 276 or embodiment 277, wherein        said detection is carried out in a dot blot format, a slot blot        format, a microarray format, a sandwich assay format, a primer        extension format, or fluorescence resonance energy transfer        (FRET).    -   279. The method of embodiment 266, wherein said hybridization is        carried out under conditions where said labeled probe hybridizes        with a viral sequence that is at least 50% homologous with said        labeled nucleic acid probe sequence.    -   280. The method of embodiment 279, wherein said hybridization is        carried out under conditions where said labeled probe hybridizes        with a viral sequence that is at least 75% homologous with said        labeled nucleic acid probe sequence.    -   281. The method of embodiment 280, wherein said hybridization is        carried out under conditions where said labeled probe hybridizes        with a viral sequence that is at least 90% homologous with said        labeled nucleic acid probe sequence.    -   282. The method of embodiment 266, wherein said labeled nucleic        acid probe comprises one or more sequences derived from        Herpesvirus saimiri A, Herpesvirus saimiri B or Herpesvirus        saimiri C.    -   283. A method of detecting the presence of viral target        sequences in a human clinical sample comprising the steps of:    -   a. providing        -   i. a human clinical sample suspected of containing nucleic            acids comprising viral target sequences,        -   ii. a labeled nucleic acid probe comprising one or more            sequences derived from a virus related to Herpesvirus            saimiri, wherein said related virus has at least 50% nucleic            acid sequence homology with Herpesvirus saimiri,    -   b. contacting said clinical sample (i) with said labeled nucleic        acid probe (ii),    -   c. allowing hybridization to take place between said labeled        nucleic acid probe (ii) and nucleic acids with viral sequences        in said clinical sample (i) if said viral target sequence        nucleic acids are present, and    -   d. detecting hybridization of said nucleic acid probe (ii) to        nucleic acids in said clinical sample (i).    -   284. The method of embodiment 283, wherein said hybridization is        carried out under conditions where said labeled probe hybridizes        with a viral sequence that is at least 75% homologous with said        labeled nucleic acid probe sequence.    -   285. The method of embodiment 284, wherein said hybridization is        carried out under conditions where said labeled probe hybridizes        with a viral sequence that is at least 90% homologous with said        labeled nucleic acid probe sequence.    -   286. The method of embodiment 283, wherein said viral target        sequence comprises mRNA.    -   287. The method of embodiment 283, wherein said viral target        sequence comprises DNA.    -   288. The method of embodiment 283, wherein said nucleic acid        probe is labeled with a is a radioactive label, a fluorescent        label, a chemiluminescent label, a hapten label, an enzymatic        label, a labeled binding partner label, a chromogenic label, or        an energy transfer pair.    -   289. The method of embodiment 288, wherein said labeled binding        partner is biotin, avidin or streptavidin.    -   290. The method of embodiment 283, wherein said nucleic acid        probe comprises a nucleotide analogue.    -   291. The method of embodiment 283, wherein said human clinical        sample is selected from blood, tissue, lavage, and combinations        thereof.    -   292. The method of embodiment 291, wherein said tissue sample is        a lung biopsy.    -   293. The method of embodiment 291, wherein said clinical sample        comprises a paraffin embedded slide.    -   294. The method of embodiment 283, wherein said method of        detection comprises in situ hybridization or flow cytometry.    -   295. The method of embodiment 283, wherein said providing step        comprises isolation of nucleic acids from said clinical sample.    -   296. The method of embodiment 295, further comprising a nucleic        acid amplification step.    -   297. The method of embodiment 296, wherein said amplification        step is carried out by an Eberwine amplification, a polymerase        chain reaction (PCR) amplification, an AmpiProbe® amplification,        a real time polymerase chain reaction (RT-PCR) amplification, a        degenerate oligonucletotide primer PCR (DOP-PCR) amplification,        a multiple displacement amplification, a self-sustained sequence        reaction (3SR) amplification, a nucleic acid based transcription        assay (NASBA) amplification, a transcription mediated        amplification (TMA), a strand displacement amplification (SDA),        a helicase-dependent amplification (HDA), a loop-mediated        isothermal amplification (LAMP), a stem-loop amplification, a        signal mediated amplification of RNA technology (SMART), an        isothermal multiple displacement amplification (IMDA), a single        primer isothermal amplification (SPIA), or a circular        helicase-dependent amplification (cHDA).    -   298. The method of embodiment 296 or embodiment 297, wherein        said detection is carried out by gel electrophoresis, in a dot        blot format, a slot blot format, a microarray format, a sandwich        assay format, a primer extension format, fluorescence resonance        energy transfer (FRET) or by fluorescence derived from        intercalation of a dye.    -   299. The method of embodiment 283, wherein said labeled nucleic        acid probe comprises one or more sequences derived from        Herpesvirus saimiri A, Herpesvirus saimiri B or Herpesvirus        saimiri C.    -   300. A method of diagnosing idiopathic pulmonary fibrosis in a        human patient comprising the steps of:    -   a. providing        -   i. a human clinical sample suspected of having idiopathic            pulmonary fibrosis,        -   ii. a labeled nucleic acid probe comprising one or more            sequences derived from Herpesvirus saimiri or a virus            related to Herpesvirus saimiri, wherein said related virus            has at least 50% nucleic acid sequence homology with            Herpesvirus saimiri,    -   b. contacting said clinical sample (i) with said labeled nucleic        acid probe (ii),    -   c. allowing hybridization to take place between said labeled        nucleic acid probe (ii) and viral sequences in said clinical        sample (i) if present, and    -   d. detecting hybridization of said nucleic acid probe (ii) to        said viral sequences in the clinical sample (i), and    -   thereby diagnosing said patient as having idiopathic pulmonary        fibrosis.    -   301. The method of embodiment 300, wherein said viral sequences        comprise mRNA.    -   302. The method of embodiment 300, wherein said viral sequences        comprise DNA.    -   303. The method of embodiment 300, wherein said nucleic acid        probe is labeled with a radioactive label, a fluorescent label,        a chemiluminescent label, a hapten label, an enzymatic label, a        labeled binding partner label, a chromogenic label, or an energy        transfer pair.    -   304. The method of embodiment 303, wherein said labeled binding        partner is biotin, avidin or streptavidin.    -   305. The method of embodiment 303, wherein said nucleic acid        probe comprises a nucleotide analogue.    -   306. The method of embodiment 300, wherein said human clinical        sample is selected from blood, tissue, lavage, and combinations        thereof.    -   307. The method of embodiment 306, wherein said tissue sample is        a lung biopsy.    -   308. The method of embodiment 307, wherein said clinical sample        comprises a paraffin embedded slide.    -   309. The method of embodiment 300, wherein said method of        detection comprises in situ hybridization or flow cytometry.    -   310. The method of embodiment 300, wherein said providing step        comprises isolation of nucleic acids from said clinical sample.    -   311. The method of embodiment 310, further comprising a nucleic        acid amplification step.    -   312. The method of embodiment 310, wherein said amplification        step is carried out by an Eberwine amplification, a polymerase        chain reaction (PCR) amplification, an AmpiProbe® amplification,        a real time polymerase chain reaction (RT-PCR) amplification, a        degenerate oligonucletotide primer PCR (DOP-PCR) amplification,        a multiple displacement amplification, a self-sustained sequence        reaction (3SR) amplification, a nucleic acid based transcription        assay (NASBA) amplification, a transcription mediated        amplification (TMA), a strand displacement amplification (SDA),        a helicase-dependent amplification (HDA), a loop-mediated        isothermal amplification (LAMP), a stem-loop amplification, a        signal mediated amplification of RNA technology (SMART), an        isothermal multiple displacement amplification (IMDA), a single        primer isothermal amplification (SPIA), or a circular        helicase-dependent amplification (cHDA).    -   313. The method of embodiment 311 or embodiment 312, wherein        said detection is carried out in a dot blot format, a slot blot        format, a microarray format, a sandwich assay format, a primer        extension format, or fluorescence resonance energy transfer        (FRET).    -   314. The method of embodiment 300, wherein said hybridization is        carried out under conditions where said labeled probe hybridizes        with a viral sequence that is at least 75% homologous with said        labeled nucleic acid probe sequence.    -   315. The method of embodiment 314, wherein said hybridization is        carried out under conditions where said labeled probe hybridizes        with a viral sequence that is at least 90% homologous with said        labeled nucleic acid probe sequence.    -   316. The method of embodiment 300, wherein said labeled nucleic        acid probe comprises one or more sequences derived from        Herpesvirus saimiri A, Herpesvirus saimiri B or Herpesvirus        saimiri C.    -   317. A method of diagnosing idiopathic pulmonary fibrosis in a        human patient comprising the steps of:    -   a. providing        -   i. a human clinical sample suspected of having a viral            infection,        -   ii. antibodies to at least two protein targets selected from            DHFR, cyclin D, IL-17 and thymidylate synthase;    -   b. contacting said clinical sample (i) with said antibodies        (ii),    -   c. allowing binding to take place between said antibodies (ii)        and proteins in said clinical sample (i) if present, and    -   d. detecting binding of said antibodies (ii) and proteins in        said clinical sample, if present, (i), and    -   thereby diagnosing said patient as having idiopathic pulmonary        fibrosis.    -   318. The method of embodiment 317, wherein said antibodies (ii)        are labeled.    -   319. The method of embodiment 317, wherein said antibodies (ii)        are detected by binding labeled secondary antibodies to said        antibodies (ii).    -   320. The method of embodiment 318 or embodiment 319, wherein        said label is a radioactive label, a fluorescent label, a        chemiluminescent label, a hapten label, an enzymatic label, a        labeled binding partner label, a chromogenic label, or an energy        transfer pair.    -   321. The method of embodiment 317, wherein said antibodies are        monoclonal antibodies, polyclonal antibodies or combinations        thereof    -   322. The method of embodiment 321, wherein said antibodies are        polyclonal antibodies.    -   323. The method of embodiment 317, wherein said antibodies are        human antibodies, humanized antibodies or combinations thereof.    -   324. A method of diagnosing idiopathic pulmonary fibrosis in a        human subject comprising the steps of    -   a. providing        -   i. a clinical sample from a subject who may have idiopathic            pulmonary fibrosis,        -   ii. one or more antibodies to viral proteins expressed by            Herpesesvirus saimiri or a virus related to Herpesvirus            saimiri, wherein said related virus has as at least 50%            nucleic acid homology with Herpesvirus saimiri    -   b. contacting said clinical sample (i) with said one or more        antibodies (ii),    -   c. allowing binding to take place between said one or more        antibodies (ii) and said clinical sample (i), and    -   d. detecting the binding of said one or more antibodies (ii) to        said viral proteins in said clinical sample (i) and thereby        diagnosing said subject as having idiopathic pulmonary fibrosis.    -   325. The method of embodiment 324 wherein one of said viral        proteins is IL-17.    -   326. The method of embodiment 324 wherein one of said viral        proteins is DHFR.    -   327. The method of embodiment 324 wherein one of said viral        proteins is cyclin D.    -   328. The method of embodiment 324 wherein one of said viral        proteins is thymidylate synthase.    -   329. The method of embodiment 324 wherein one of said viral        proteins is a viral capsid protein.    -   330. A method of treating idiopathic pulmonary fibrosis in a        subject comprising administering to said subject, one or more        antibodies to one or more viral proteins expressed by        Herpesvirus saimiri or a virus related to Herpesvirus saimiri        wherein said related virus has at least 50% nucleic acid        homology with Herpesvirus saimiri.    -   331. The method of embodiment 330 wherein one of said viral        proteins is IL-17.    -   332. The method of embodiment 300 wherein one of said viral        proteins is DHFR.    -   333. The method of embodiment 300 wherein one of said viral        proteins is cyclin D.    -   334. The method of embodiment 330 wherein one of said viral        proteins is thymidylate synthase.    -   335. The method of embodiment 300 wherein one of said viral        proteins is a viral capsid protein.    -   336. A method of preventing idiopathic pulmonary fibrosis in a        subject comprising administering to said subject one or more        antibodies to one or more proteins expressed by Herpesvirus        saimiri or a virus related to Herpesvirus saimiri wherein said        related virus has as at least 50% nucleic acid homology with        Herpesvirus saimiri.    -   337. The method of embodiment 336 wherein one of said viral        proteins is IL-17.    -   338. The method of embodiment 336 wherein one of said viral        proteins is DHFR.    -   339. The method of embodiment 336 wherein one of said viral        proteins is cyclin D.    -   340. The method of embodiment 336 wherein one of said viral        proteins is thymidylate synthase.    -   341. The method of embodiment 336 wherein one of said viral        proteins is a viral capsid protein.    -   342. A kit for detection of viral target sequences in a human        clinical sample comprising:    -   a. a labeled nucleic acid probe selected from (i) a probe        comprising one or more sequences derived from Herpesvirus        saimiri, (ii) a probe derived from a virus related to        Herpesvirus saimiri, wherein said related virus has at least 50%        nucleic acid sequence homology with Herpesvirus saimiri, or a        combination of (i) and (ii); and    -   b. reagents for carrying out hybridization of said probe to        nucleic acids in the clinical sample.    -   343. The kit of embodiment 342, further comprising reagents for        isolating said viral target sequences.    -   344. The kit of embodiment 342 or embodiment 343, further        comprising    -   a. a primer comprising a sequence complementary to a sequence in        one strand of the viral target sequence;    -   b. a primer comprising a sequence identical to a sequence in        said strand of the viral target sequence; and    -   c. a reagent for carrying out amplification of said viral target        sequence.    -   345. The kit of embodiment 342, further comprising a nucleic        acid probe that is complementary to a viral target sequence.    -   346. The kit of embodiment 342, further comprising an        intercalator that increases fluorescence after binding to        double-stranded DNA.    -   347. The kit of embodiment 345 or embodiment 346, wherein at        least one primer or probe is labeled.    -   348. A method of detecting the presence of viral target        sequences in a human clinical sample comprising the steps of    -   a. providing a human clinical sample that may contain virally        infected cells,    -   b. means for isolating nucleic acids from said clinical sample,    -   c. means for amplification of nucleic acids in said sample,        wherein said means are capable of amplifying nucleic acids of        Herpesvirus saimiri or a virus related to Herpesvirus saimiri        wherein said related virus has at least 50% nucleic acid        homology with Herpesvirus saimiri when said sample comprises        nucleic acids of Herpesvirus saimiri or said related virus,    -   d. isolating nucleic acids from said clinical sample by said        means (ii),    -   e. combining said isolated nucleic acids with said amplification        means (iii),    -   f. amplifying said nucleic acids from Herpesvirus saimiri or        said related virus, and    -   g. detecting the amplification of said nucleic acids of        Herpesvirus saimiri or said related virus, thereby detecting the        presence of said viral target sequences.    -   349. The embodiment of claim 348, wherein said means for        amplification includes reagents for performing an Eberwine        amplification, a polymerase chain reaction (PCR) amplification,        an AmpiProbe® amplification, a real time polymerase chain        reaction (RT-PCR) amplification, a degenerate oligonucletotide        primer PCR (DOP-PCR) amplification, a multiple displacement        amplification, a self-sustained sequence reaction (3SR)        amplification, a nucleic acid based transcription assay (NASBA)        amplification, a transcription mediated amplification (TMA), a        strand displacement amplification (SDA), a helicase-dependent        amplification (HDA), a loop-mediated isothermal amplification        (LAMP), a stem-loop amplification, a signal mediated        amplification of RNA technology (SMART), an isothermal multiple        displacement amplification (IMDA), a single primer isothermal        amplification (SPIA), or a circular helicase-dependent        amplification (cHDA). The method of claim 348, wherein said        detecting step (vii) is carried out using labeled nucleotides, a        labeled primer, a labeled probe, an intercalating dye or a        combination thereof.    -   350. The method of embodiment 348, wherein said detecting        step (g) is carried out using one or more labeled nucleotides,        one or more labeled primers, one or more labeled probes, one or        more intercalating dyes or a combination thereof.    -   351. A kit for detecting at least two protein targets selected        from DHFR, cyclin D, IL-17 and thymidylate synthase in a human        clinical sample comprising:    -   a. an antibody to any two of DHFR, cyclin D, IL-17 and        thymidilyate synthase; and    -   b. reagents for the binding of said antibodies to proteins in        said sample.    -   352. The kit of embodiment 351, wherein said antibodies are        monoclonal antibodies, polyclonal antibodies, or combinations        thereof.    -   353. The kit of embodiment 351, wherein said antibody is        labeled.    -   354. The kit of embodiment 351, further comprising a secondary        antibody.    -   355. The kit of embodiment 354, wherein the secondary antibody        is labeled.    -   356. The kit of embodiment 351, wherein the secondary antibody        is conjugated to an enzyme.    -   357. The kit of claim 356, further comprising reagents for        signal amplification, wherein said signal amplification.    -   358. A composition comprising a viral target sequence hybridized        to (i) a non-radioactively labeled nucleic acid comprising one        or more sequences derived from Herpesvirus saimiri, (ii) a        non-radioactively labeled nucleic acid comprising one or more        sequences derived from a virus related to Herpesvirus saimiri,        wherein said related virus has at least 50% nucleic acid        sequence homology with Herpesvirus saimiri, or a combination        thereof, wherein said hybridization product is in a human cell        of a clinical sample.    -   359. A method of diagnosing idiopathic pulmonary fibrosis in a        human patient comprising the steps of:    -   a. providing        -   i. a human clinical sample suspected of having a viral            infection,        -   ii. an antibody to viral IL-17,    -   b. contacting said clinical sample (i) with said antibody (ii),    -   c. allowing binding to take place between said antibody (ii) and        proteins in said clinical sample (i) if present, and    -   d. detecting binding of said antibody (ii) to said viral IL-17        in said clinical sample (i), and thereby diagnosing said patient        as having idiopathic pulmonary fibrosis.    -   360. A method of diagnosing Castleman's disease, a lymphoma, a        thymoma and a sarcoma in a human patient comprising the steps        of:    -   a. providing        -   i. a human clinical sample suspected of having Castleman's            disease, a lymphoma, a thymoma and a sarcoma,        -   ii. a labeled nucleic acid probe comprising one or more            sequences derived from Herpesvirus saimiri,    -   b. contacting said clinical sample (i) with said labeled nucleic        acid probe (ii),    -   c. allowing hybridization to take place between said labeled        nucleic acid probe (ii) and viral sequences in said clinical        sample (i) if present, and    -   d. detecting hybridization of said nucleic acid probe (ii) to        said viral sequences in said clinical sample (i), and    -   thereby diagnosing said patient as Castleman's disease, a        lymphoma, a thymoma or a sarcoma.    -   361. The method of embodiment 360, wherein said viral sequences        comprise mRNA.    -   362. The method of embodiment 360, wherein said viral sequences        comprise DNA.    -   363. The method of embodiment 360, wherein said viral sequences        comprise U rich non-coding RNA.    -   364. The method of embodiment 360, wherein said nucleic acid        probe is labeled with a radioactive label, a fluorescent label,        a chemiluminescent label, a hapten label, an enzymatic label, a        labeled binding partner label, a chromogenic label, or an energy        transfer pair.    -   365. The method of embodiment 364, wherein said labeled binding        partner is biotin, avidin or streptavidin.    -   366. The method of embodiment 360, wherein said nucleic acid        probe comprises a nucleotide analogue.    -   367. The method of embodiment 360, wherein said human clinical        sample is selected from blood, tissue, and combinations thereof    -   368. The method of embodiment 367, wherein said clinical sample        comprises a paraffin embedded slide.    -   369. The method of embodiment 360, wherein said method of        detection comprises in situ hybridization or flow cytometry.    -   370. The method of embodiment 360, wherein said providing step        comprises isolation of nucleic acids from said clinical sample.    -   371. The method of embodiment 360, further comprising a nucleic        acid amplification step.    -   372. The method of embodiment 360, wherein said amplification        step is carried out by an Eberwine amplification, a polymerase        chain reaction (PCR) amplification, an AmpiProbe® amplification,        a real time polymerase chain reaction (RT-PCR) amplification, a        degenerate oligonucletotide primer PCR (DOP-PCR) amplification,        a multiple displacement amplification, a self-sustained sequence        reaction (3SR) amplification, a nucleic acid based transcription        assay (NASBA) amplification, a transcription mediated        amplification (TMA), a strand displacement amplification (SDA),        a helicase-dependent amplification (HDA), a loop-mediated        isothermal amplification (LAMP), a stem-loop amplification, a        signal mediated amplification of RNA technology (SMART), an        isothermal multiple displacement amplification (IMDA), a single        primer isothermal amplification (SPIA), or a circular        helicase-dependent amplification (cHDA).    -   373. The method of embodiment 371 or embodiment 372, wherein        said detection is carried out in a dot blot format, a slot blot        format, a microarray format, a sandwich assay format, a primer        extension format, or fluorescence resonance energy transfer        (FRET).    -   374. The method of embodiment 360, wherein said hybridization is        carried out under conditions where said labeled probe hybridizes        with a viral sequence that is at least 75% homologous with said        labeled nucleic acid probe sequence.    -   375. The method of embodiment 374, wherein said hybridization is        carried out under conditions where said labeled probe hybridizes        with a viral sequence that is at least 90% homologous with said        labeled nucleic acid probe sequence.    -   376. The method of embodiment 360, wherein said labeled nucleic        acid probe comprises one or more sequences derived from        Herpesvirus saimiri A, Herpesvirus saimiri B or Herpesvirus        saimiri C.    -   377. A method of diagnosing Castleman's disease, a lymphoma, a        thyoma and a sarcoma in a human patient comprising the steps of:    -   a. providing        -   i. a human clinical sample suspected of having Castleman's            disease, a lymphoma, a thyoma and a sarcoma,        -   ii. a labeled nucleic acid probe comprising one or more            sequences derived from a virus related to Herpesvirus            saimiri, wherein said related virus has at least 50% nucleic            acid sequence homology with Herpesvirus saimiri,    -   b. contacting said clinical sample (i) with said labeled nucleic        acid probe (ii),    -   c. allowing hybridization to take place between said labeled        nucleic acid probe (ii) and viral sequences in said clinical        sample (i) if present, and    -   d. detecting hybridization of said nucleic acid probe (ii) to        said viral sequences in said clinical sample (i), and    -   thereby diagnosing said patient as Castleman's disease, a        lymphoma, a thymoma or a sarcoma.    -   378. The method of embodiment 377, wherein said hybridization is        carried out under conditions where said labeled probe hybridizes        with a viral sequence that is at least 75% homologous with said        labeled nucleic acid probe sequence.    -   379. The method of embodiment 378, wherein said hybridization is        carried out under conditions where said labeled probe hybridizes        with a viral sequence that is at least 90% homologous with said        labeled nucleic acid probe sequence.    -   380. The method of embodiment 377, wherein said viral sequences        comprise mRNA.    -   381. The method of embodiment 377, wherein said viral sequences        comprise DNA.    -   382. The method of embodiment 377, wherein said viral sequences        comprise U rich non-coding RNA.    -   383. The method of embodiment 377, wherein said nucleic acid        probe is labeled with a radioactive label, a fluorescent label,        a chemiluminescent label, a hapten label, an enzymatic label, a        labeled binding partner label, a chromogenic label, or an energy        transfer pair.    -   384. The method of embodiment 383, wherein said labeled binding        partner is biotin, avidin or streptavidin.    -   385. The method of embodiment 377, wherein said nucleic acid        probe comprises a nucleotide analogue.    -   386. The method of embodiment 377, wherein said human clinical        sample is selected from blood, tissue, and combinations thereof    -   387. The method of embodiment 386, wherein said clinical sample        comprises a paraffin embedded slide.    -   388. The method of embodiment 377, wherein said method of        detection comprises in situ hybridization or flow cytometry.    -   389. The method of embodiment 377, wherein said providing step        comprises isolation of nucleic acids from said clinical sample.    -   390. The method of embodiment 389, further comprising a nucleic        acid amplification step.    -   391. The method of embodiment 390, wherein said amplification        step comprises an Eberwine amplification, a polymerase chain        reaction (PCR) amplification, an AmpiProbe® amplification, a        real time polymerase chain reaction (RT-PCR) amplification, a        degenerate oligonucletotide primer PCR (DOP-PCR) amplification,        a multiple displacement amplification, a self-sustained sequence        reaction (3SR) amplification, a nucleic acid based transcription        assay (NASBA) amplification, a transcription mediated        amplification (TMA), a strand displacement amplification (SDA),        a helicase-dependent amplification (HDA), a loop-mediated        isothermal amplification (LAMP), a stem-loop amplification, a        signal mediated amplification of RNA technology (SMART), an        isothermal multiple displacement amplification (IMDA), a single        primer isothermal amplification (SPIA), or a circular        helicase-dependent amplification (cHDA).    -   392. The method of embodiment 390 or embodiment 391, wherein        said detection is carried out in a dot blot format, a slot blot        format, a microarray format, a sandwich assay format, a primer        extension format, or fluorescence resonance energy transfer        (FRET).    -   393. A kit for detection of viral target sequences in a human        clinical sample comprising:    -   a. a labeled nucleic acid probe selected from (i) a        non-radioactively labeled probe comprising one or more sequences        derived from Herpesvirus saimiri, (ii) a probe derived from a        virus related to Herpesvirus saimiri, wherein said related virus        has at least 50% nucleic acid sequence homology with Herpesvirus        saimiri, or a combination of (i) and (ii); and    -   b. reagents for carrying out hybridization of said probe to a        clinical sample.    -   394. The kit of embodiment 393, further comprising reagents for        isolating said viral target sequences.    -   395. A kit comprising:    -   a. a labeled nucleic acid probe selected from (i) a        non-radioactively labeled probe comprising one or more sequences        derived from Herpesvirus saimiri, (ii) a probe derived from a        virus related to Herpesvirus saimiri, wherein said related virus        has at least 50% nucleic acid sequence homology with Herpesvirus        saimiri, or a combination of (i) and (ii);    -   b. reagents for carrying out hybridization of said probe to a        clinical sample,    -   c. a primer comprising a sequence complementary to a sequence in        one strand of the viral target sequence;    -   d. a primer comprising a sequence identical to a sequence in        said strand of the viral target sequence; and    -   e. a reagent for carrying out amplification of said viral target        sequence.    -   396. A method of diagnosing Castleman's disease, a lymphoma, a        thymoma and a sarcoma in a human patient in a human patient        comprising the steps of:    -   a. providing        -   i. a human clinical sample suspected of having a viral            infection,        -   ii. antibodies to at least two protein targets selected from            DHFR, cyclin D, IL-17 and thymidylate synthase;    -   b. contacting said clinical sample (i) with said antibodies        (ii),    -   c. allowing binding to take place between said antibodies (ii)        and proteins in said clinical sample (i) if present, and    -   d. detecting binding of said antibodies (ii) to said proteins in        said clinical sample (i), and    -   thereby diagnosing said patient as having idiopathic pulmonary        fibrosis.    -   397. The method of embodiment 396, wherein said antibodies (ii)        are labeled.    -   398. The method of embodiment 396, wherein said antibodies (ii)        are detected by binding labeled secondary antibodies to said        antibodies (ii).    -   399. The method of embodiment 397 or embodiment 398, wherein        said label is a radioactive label, a fluorescent label, a        chemiluminescent label, a hapten label, an enzymatic label, a        labeled binding partner label, a chromogenic label, or an energy        transfer pair.    -   400. The method of embodiment 396, wherein said antibodies are        monoclonal antibodies, polyclonal antibodies or combinations        thereof    -   401. The method of embodiment 400, wherein said antibodies are        polyclonal antibodies.    -   402. The method of embodiment 400, wherein said antibodies are        human antibodies, humanized antibodies or combinations thereof.    -   403. A method of isolating a clone comprising a gamma        Herpesvirus sequence comprising the steps of    -   a. providing        -   i. a biological sample from a subject who has idiopathic            pulmonary fibrosis, idiopathic Castleman's disease, a            retroperitoneal liposarcoma, a thymoma or a mediastinal            lymphoma,        -   ii. reagents for isolating gamma Herpesvirus nucleic acids            from said biological sample,        -   iii. reagents for creating a clone library of said isolated            nucleic acids,        -   iv. a nucleic acid probe or probes comprising one or more            gamma Herpesvirus sequences,    -   b. isolating gamma Herpesvirus nucleic acids from said        biological sample;    -   c. creating a clone library of nucleic acid constructs from said        isolated gamma Herpesvirus nucleic acids,    -   d. hybridizing said nucleic acid probe or probes (iv),    -   e. screening said clone library (c) to identify a clone that        comprises nucleic acids having homology with said nucleic acid        probe or probes (c1), and    -   f. isolating said clone identified in step e.    -   404. The method of embodiment 403, wherein said nucleic acids        from said biological sample are DNA.    -   405. The method of embodiment 403, wherein said nucleic acids        from said biological sample are RNA.    -   406. The method of embodiment 403 wherein said probe or probes        comprises a Herpesvirus saimiri STP sequence, a Herpesvirus        saimiri Terminal Repeat sequence, a Herpesvirus saimiri IL-17        sequence, a Herpesvirus saimiri DNA polymerase sequence,        Herpesvirus saimiri cyclin D sequence, a Herpesvirus saimiri        IL-17 sequence, a Herpesvirus saimiri glycoprotein B sequence, a        Herpesvirus saimiri terminase sequence, or any combination        thereof.    -   407. The method of embodiment 403, further comprising a step of        carrying out subtractive hybridization step prior to step c.    -   408. The method of embodiment 403, further comprising a step of        carrying out positive selection step prior to step c.    -   409. The method of embodiment 403, further comprising a step of        enriching episomal DNA apart from chromosomal DNA prior to step        c.    -   410. The method of embodiment 403, further comprising after        step e. the steps of f. obtaining the nucleic acid sequence of        said gamma Herpesvirus clone; and g. comparing the sequence of        said clone to the sequence of Herpesvirus saimiri.    -   411. The method of embodiment 410, further comprising after        step g. a step of h. synthesizing nucleic acids using said gamma        Herpesvirus DNA sequence.    -   412. The method of embodiment 411, further comprising after        step h. a step of i. labeling said synthesized nucleic acids.    -   413. The method of embodiment 403, further comprising after        step e. the steps of f. isolating said nucleic acid construct        from said clone and g. labeling the nucleic acids of said        construct.    -   414. The method of embodiment 412 or embodiment 413, wherein        said nucleic acid construct has a phage promoter, and said        method further comprises a step of isolating said nucleic acid        construct from said clone, and a step of carrying out an RNA        transcription step with said construct as a template.    -   415. The method of embodiment 414, wherein said transcripts are        labeled during said transcription step.    -   416. The method of embodiment 413 or embodiment 415, wherein        said label is a non-radioactive label selected from a        fluorescent label, a chemiluminescent label, a hapten label, a        chromogenic label, or an energy transfer pair.    -   417. A method of isolating a nucleic acid comprising a gamma        Herpesvirus sequence comprising the steps of:    -   a. providing        -   i. biological sample from a subject who has idiopathic            pulmonary fibrosis, idiopathic Castleman's disease, a            retroperitoneal liposarcoma, a thymoma or a mediastinal            lymphoma,        -   ii. a reagent for isolating nucleic acids from said            biological sample,        -   iii. nucleic acid primers that are capable of amplifying            multiple gamma Herpesvirus species in a PCR reaction, and        -   iv. reagents for carrying out a PCR reaction,    -   b. isolating nucleic acids from said biological sample,    -   c. mixing said nucleic acid primers, and said PCR reagent with        said biological sample,    -   d. carrying out a PCR reaction,    -   e. analyzing said PCR reaction, and    -   f. identifying the presence of an amplification product.    -   418. The method of embodiment 417, wherein said nucleic acids        from said biological sample are DNA.    -   419. The method of embodiment 417, wherein said nucleic acids        from said biological sample are RNA.    -   420. The method of embodiment 417, wherein said nucleic acid        primers amplify a gamma Herpesvirus DNA polymerase gene, a gamma        Herpesvirus glycoprotein B gene, a gamma Herpesvirus terminase        gene or a combination thereof    -   421. The method of embodiment 417, further comprising a step of        carrying out subtractive hybridization step prior to step c.    -   422. The method of embodiment 417, further comprising a step of        carrying out positive selection prior to step c.    -   423. The method of embodiment 417, further comprising a step of        enriching episomal DNA apart from chromosomal DNA prior to step        c.    -   424. The method of embodiment 417, further comprising the        steps g. of obtaining the nucleic acid sequence of said nucleic        acid comprising a gamma Herpesvirus sequence, and h. comparing        the sequence of said clone to the sequence of Herpesvirus        saimiri after step f.    -   425. The method of embodiment 424 further comprising a step        of i. synthesizing nucleic acids using the DNA sequence of said        gamma Herpesvirus clone.    -   426. The method of embodiment 425, further comprising the steps        of j. generating a nucleic acid construct using the DNA sequence        of said gamma Herpesvirus clone; and k. transfecting cells to        obtain a clone of said gamma Herpesvirus DNA sequence.    -   427. The method of embodiment 417, further comprising the steps        of generating of a nucleic acid construct from said PCR products        and transfecting cells to obtain a clone of said PCR product        after step f.    -   428. The method of embodiment 425, wherein the synthesized        nucleic acid comprises at least one non-radioactive label        selected from a fluorescent label, a chemiluminescent label, a        hapten label, a chromogenic label, or an energy transfer pair.    -   429. The method of embodiment 426, further comprising the steps        isolating said construct from said clone and labeling the        nucleic acids of said construct.    -   430. The method of embodiment 427, further comprising the steps        isolating said construct from said clone and labeling the        nucleic acids of said construct.    -   431. The method of embodiment 426 or embodiment 427, wherein        said construct has a phage promoter, and said method further        comprises the steps of isolating said construct from said clone        and carrying out an RNA transcription step with said clone as a        template.    -   432. The method of embodiment 431 where said transcripts are        labeled during said transcription step.    -   433. A clone comprising DNA sequences from a gamma Herpesvirus        DNA produced by the method of embodiment 403.    -   434. A clone comprising DNA sequences from a gamma Herpesvirus        produced by the method of embodiment 427.    -   435. A clone comprising DNA sequences from a gamma Herpesvirus        produced by the method of embodiment 428.    -   436. A method for diagnosing idiopathic pulmonary fibrosis,        idiopathic Castleman's disease, a retroperitoneal liposarcoma, a        thymoma or a mediastinal lymphoma in a subject comprising    -   a. providing        -   i. a human clinical sample suspected of having idiopathic            pulmonary fibrosis, Castleman's disease, a lymphoma, a            thymoma and a sarcoma,        -   ii. a labeled nucleic acid probe of embodiment 412, 413,            433, 434 or 435,    -   b. contacting said clinical sample (i) with said labeled nucleic        acid probe (ii),    -   c. allowing hybridization to take place between said labeled        nucleic acid probe (ii) and viral sequences in said clinical        sample (i) if present, and    -   d. detecting hybridization of said nucleic acid probe (ii) to        said viral sequences in said clinical sample (i), and thereby        diagnosing said patient as having idiopathic pulmonary fibrosis,        Castleman's disease, a lymphoma, a thymoma or a sarcoma.    -   437. A method of diagnosing idiopathic pulmonary fibrosis,        idiopathic Castleman's disease, a retroperitoneal liposarcoma, a        thymoma or a mediastinal lymphoma in a subject comprising    -   a. providing        -   i. a human clinical sample suspected of having idiopathic            pulmonary fibrosis, Castleman's disease, a lymphoma, a            thymoma and a sarcoma, and        -   ii. reagents for amplification of viral nucleic acids in            said sample of embodiment 410, 412 or 424,    -   b. contacting said clinical sample (i) with said reagents for        amplification (ii),    -   c. amplifying nucleic acids in said clinical sample (i),    -   d. allowing hybridization to take place between the viral        nucleic acids amplified in step c and a labeled nucleic acid        probe of embodiment 412, 413, 433, 434 or 435,    -   e. detecting hybridization of said nucleic acid probe of        embodiment 412, 413, 433, 434 or 435 to said amplified nucleic        acids produced in step c,    -   thereby diagnosing said patient as having idiopathic pulmonary        fibrosis, Castleman's disease, a lymphoma, a thymoma or a        sarcoma.    -   438. A method of diagnosing Castleman's disease, a lymphoma, a        thymoma or a sarcoma in a human patient comprising the steps of:    -   a. providing        -   i. a human clinical sample suspected of having Castleman's            disease, a lymphoma, a thymoma or a sarcoma,        -   ii. reagents for isolation of nucleic acids from said            clinical sample,        -   iii. reagents for carrying out nucleic acid amplification,        -   iv. primers that are capable of amplifying nucleic acid            sequences of gamma Herpesvirus targets that have at least            50% homology with Herpesvirus saimiri    -   b. isolating nucleic from said sample (i) with said reagents        (ii)    -   c. mixing said isolated nucleic acids from step (b) with said        amplification reagents (ii) and said primers (iii),    -   d. carrying out nucleic acid amplification if said gamma        Herpesvirus targets are present in said clinical sample (i),    -   e. detecting the presence of amplified products form step (d).    -   439. A method of treating a human patient suffering from a        disease associated with a gamma Herpesvirus infection wherein        said disease is selected from idiopathic pulmonary fibrosis,        Castleman's disease, a lymphoma, a thymoma or a sarcoma        comprising the step of administering a therapeutically effective        amount of an agent selected from an agent that inhibits        propagation of the virus, an agent that inhibits replication of        the virus, an agent that down-regulates expression of a        virus-specific protein, an antibody neutralizes a viral protein,        an agent that blocks virus entry into host cells, and an agent        that inhibits a viral enzyme.    -   440. The method of embodiment 439, wherein said agent is an        antibody that binds to viral IL-17.    -   441. The composition of embodiment 358, wherein said labeled        nucleic acid is partially hybridized to said one or more        sequences derived from Herpesvirus saimiri.    -   442. The composition of embodiment 358, wherein said labeled        nucleic acid has more than 50% homology to said one or more        sequences derived from Herpesvirus saimiri.    -   443. The composition of embodiment 358, wherein said labeled        nucleic acid comprises one or more nucleotide analogues.    -   444. The composition of embodiment 443, wherein said one or more        nucleotide analogues confers a property to said labeled nucleic        acid selected from differential melting, a detectable signal,        and maintenance of stable hybridization with a nucleic acid that        is not completely complementary to said labeled nucleic acid.    -   445. A method of identifying a compound for the treatment of        idiopathic pulmonary fibrosis comprising the steps of    -   (a) administering a compound to a severe combined        immunodifficient (“SCID”) mouse having fibroblast cells from a        patient suffering from idiopathic pulmonary fibrosis,    -   (b) measuring in a sample from said mouse a level of one or more        proteins selected from IL-17, cyclin D, DHFR, thymidylate        synthase, and combinations thereof, and    -   (c) comparing said level of one or more proteins in step (b)        with a level of said one or more proteins measured in a sample        from a SCID mouse having fibroblast cells from a patient        suffering from idiopathic pulmonary fibrosis that has not been        exposed to the compound, wherein a level of said one or more        proteins measured in step (b) that is lower than a level of said        one or more proteins measured in step (c) identifies a compound        for treating idiopathic pulmonary fibrosis.    -   446. The method of embodiment 445, further comprising before        step (a) the steps of isolating fibroblast cells from a patient        suffering from idiopathic pulmonary fibrosis, and passaging said        cells.    -   447. The method of embodiment 445, wherein said sample is        selected from blood cells, lung cells, lung tissue or lungs.    -   448. The method of embodiment 445, wherein said measuring        step (b) is carried out by immunohistochemistry.    -   449. The method of embodiment 445, wherein said measuring        step (b) is carried out by an immunoassay.    -   450. The method of embodiment 449, wherein said immunoassay is        selected from a competitive homogeneous immunoassay, a        competitive heterogeneous immunoassay, a one-site noncompetitive        homogenous assay and a two-site noncompetitive homogenous assay.    -   451. The method of embodiment 450, wherein said immunoassay is        selected from a radioimmunoassay, a Luminex® assay, a microarray        assay, a fluorescence polarization immunoassay, an immunoassay        comprising a Förster resonance energy transfer (FRET) signaling        system and an enzyme immunoassay.    -   452. The method of embodiment 445, wherein said measuring        step (b) is carried out by measuring an amount of mRNA molecules        coding for said one or more proteins in said sample.    -   453. The method of embodiment 452, wherein said amount of mRNA        is measured using a microarray. 454. The method of embodiment        100, wherein said compound for the treatment of idiopathic        pulmonary fibrosis is an antibody.    -   455. The method of embodiment 454, wherein said antibody has        selective affinity for IL-17, cyclin D, DHFR, or thymidylate        synthase.    -   456. The method of embodiment 454, wherein said antibody has        selective affinity for TGF-β, TGF-β receptor, IL-23, IL-23        receptor, or IL-1β.    -   457. The method of embodiment 445 wherein said compound is a        small molecule.    -   458. The method of embodiment 457, wherein said small molecule        is selected from an anti-viral agent, an inhibitor of viral        replication, an inhibitor of viral entry into a host cell, and a        viral enzyme inhibitor.    -   459. A method of identifying a compound for the treatment of        idiopathic pulmonary fibrosis, comprising the steps of    -   (a) administering a compound to a severe combined        immunodifficient (“SCID”) mouse having fibroblast cells from a        patient suffering from idiopathic pulmonary fibrosis,    -   (b) measuring in a sample from said mouse a level of one or more        viral markers selected from a Herpesvirus-specific nucleic acid,        a Herpesvirus-specific protein and a combination thereof, and    -   (c) comparing said level of one or more viral markers in        step (b) with a level of said one or more viral markers measured        in a sample from a SCID mouse having fibroblast cells from a        patient suffering from idiopathic pulmonary fibrosis that has        not been exposed to the compound,    -   wherein a level of said one or more viral markers measured in        step (b) that is lower than a level of said one or more viral        markers measured in step (c) identifies a compound for treating        idiopathic pulmonary fibrosis.    -   460. The method of embodiment 459, further comprising before        step (a) the steps of isolating fibroblast cells from a patient        suffering from idiopathic pulmonary fibrosis, and passaging said        cells.    -   461. The method of embodiment 459, wherein said sample is        selected from blood cells, lung cells, lung tissue or lungs.    -   462. The method of embodiment 459, wherein said viral marker is        a protein and said measuring step (b) is carried out by        immunohistochemistry.    -   463. The method of embodiment 459, wherein said viral marker is        a protein and said measuring step (b) is carried out by an        immunoassay.    -   464. The method of embodiment 463, wherein said immunoassay is        selected from a competitive homogeneous immunoassay, a        competitive heterogeneous immunoassay, a one-site noncompetitive        homogenous assay and a two-site noncompetitive homogenous assay.    -   465. The method of embodiment 464, wherein said immunoassay is        selected from a radioimmunoassay, a Luminex® assay, a microarray        assay, a fluorescence polarization immunoassay, an immunoassay        comprising a Förster resonance energy transfer (FRET) signaling        system and an enzyme immunoassay.    -   466. The method of embodiment 459, wherein said viral marker is        a nucleic acid.    -   467. The method of embodiment 466, wherein said nucleic acid is        viral DNA or viral RNA.    -   468. The method of embodiment 467, wherein said nucleic acid        comprises a sequence that codes for a protein selected from        IL-17, cyclin D1 thymidylate synthase, and dihydrofolate        reductase.    -   469. The method of embodiment 467, wherein the nucleic acid is        mRNA.    -   470. The method of embodiment 469, wherein said mRNA is measured        using a microarray.    -   471. The method of embodiment 459, wherein said compound for the        treatment of idiopathic pulmonary fibrosis is an antibody.    -   472. The method of embodiment 471, wherein said antibody has        selective affinity for IL-17, cyclin D, DHFR, or thymidylate        synthase.    -   473. The method of embodiment 471, wherein said antibody has        selective affinity for TGF-β, TGF-β receptor, IL-23, IL-23        receptor, or IL-1β.    -   474. The method of embodiment 459 wherein said compound is a        small molecule.    -   475. The method of embodiment 474, wherein said small molecule        is selected from an anti-viral agent, an inhibitor of viral        replication, an inhibitor of viral entry into a host cell, and a        viral enzyme inhibitor.    -   476. A method of isolating a viral nucleic acid sequence from a        subject suffering from idiopathic pulmonary fibrosis, comprising        the steps of    -   (a) administering fibroblast cells from a subject suffering from        idiopathic pulmonary fibrosis to a severe combined        immunodifficient (“SCID”) mouse;    -   (b) isolating cells, tissues or organs of said SCID mouse;    -   (c) isolating nucleic acids from said cells, tissues or organs        of step (b); and    -   (d) amplifying one or more nucleic acids of step (c),    -   wherein the product of step (d) is enriched for viral nucleic        acid sequences.    -   477. The method of embodiment 476, further comprising before        step (a) the steps of isolating fibroblast cells from a patient        suffering from idiopathic pulmonary fibrosis, and passaging said        cells.    -   478. The method of embodiment 476, wherein said cells are blood        cells.    -   479. The method of embodiment 476, wherein said cells, tissues        or organs are selected from blood cells, lung cells, lung tissue        or lungs.    -   480. The method of embodiment 479, wherein fibrotic material is        collected from said lung tissue or lungs.    -   481. The method of embodiment 476, wherein said amplification        step (d) is carried out with primers complementary to a        Herpesvirus saimiri nucleic acid.    -   482. The method of embodiment 476, wherein said amplification        step (d) is carried out with primers generic for        gammaherpesviruses.    -   483. The method of embodiment 476, wherein said amplification is        carried out by PCR.    -   484. The method of embodiment 476, wherein said amplification is        carried out by RT-PCR.    -   485. The method of embodiment 476, further comprising after        step (d) the steps of:    -   (e) inserting said amplified nucleic acids of step (c) into a        recombinant DNA vector to create a recombinant DNA library;    -   (f) introducing said recombinant DNA library of step (e) into        host cells;    -   (g) selecting for clones of host cells of step (f) comprising        recombinant DNA vectors; and    -   (h) screening said clones for the presence of viral sequences.    -   486. A method of isolating a viral nucleic acid sequence from a        subject suffering from idiopathic pulmonary fibrosis comprising        the steps of    -   (a) administering fibroblast cells from a subject suffering from        idiopathic pulmonary fibrosis to a severe combined        immunodeficient (“SCID”) mouse;    -   (b) isolating cells, tissues or organs of said SCID mouse; and    -   (c) isolating nucleic acids from said cells, tissues or organs        of step (b); and    -   (d) binding nucleic acids comprising viral sequences in said        isolated nucleic acids of step (c) to complementary strands of        viral DNA,    -   thereby obtaining nucleic acids that are enriched for viral        nucleic acid sequences.    -   487. The method of embodiment 486, further comprising before        step (a) the steps of isolating fibroblast cells from a patient        suffering from idiopathic pulmonary fibrosis, and passaging said        cells.    -   488. The method of embodiment 486, wherein said cells are blood        cells.    -   489. The method of embodiment 486, wherein said cells, tissues        or organs are selected from blood cells, lung cells, lung tissue        or lungs.    -   490. The method of embodiment 486, wherein fibrotic material is        collected from said lung tissue or lungs.    -   491. The method of embodiment 486, further comprising after        step (d) a step of (e) amplifying said isolated nucleic acids of        step (d).    -   492. The method of embodiment 491, wherein said amplification        step (e) is carried out with primers complementary to a        Herpesvirus saimiri nucleic acid.    -   493. The method of embodiment 491, wherein said amplification        step (e) is carried out with primers generic for        gammaherpesviruses.    -   494. The method of embodiment 491, wherein said amplification is        carried out by PCR.    -   495. The method of embodiment 491, wherein said amplification is        carried out by RT-PCR.    -   496. The method of embodiment 491, further comprising after said        amplifying step (e) the steps of:    -   (f) inserting said amplified nucleic acids of step (e) into a        recombinant DNA vector to create a recombinant DNA library;    -   (g) introducing said recombinant DNA library of step (f) into        host cells;    -   (h) selecting for clones of host cells of step (g) comprising        recombinant DNA vectors; and    -   (i) screening said clones for the presence of viral sequences.    -   497. A method of isolating a viral nucleic acid sequence from a        subject suffering from idiopathic pulmonary fibrosis, comprising        the steps of:    -   (a) administering fibroblast cells from a subject suffering from        idiopathic pulmonary fibrosis to a severe combined        immunodifficient (“SCID”) mouse;    -   (b) isolating cells, tissues or organs of said SCID mouse;    -   (c) isolating nucleic acids from said cells, tissues or organs        of step (b);    -   (d) Inserting said isolated nucleic acids of step (c) into a        recombinant DNA vector and thereby forming a library of        recombinant DNA;    -   (e) introducing said library of step (d) into host cells;    -   (f) selecting for clones comprising recombinant DNA vectors in        said host cells of step (e); and    -   (g) screening said clones of step (f) for the presence of viral        sequences.    -   498. The method of embodiment 497, further comprising before        step (a) the steps of isolating fibroblast cells from a patient        suffering from idiopathic pulmonary fibrosis, and passaging said        cells

All publications, patents, patent applications and other documents citedin this application are hereby incorporated by reference in theirentireties for all purposes to the same extent as if each individualpublication, patent, patent application or other document wereindividually indicated to be incorporated by reference for all purposes.

While various specific embodiments have been illustrated and described,it will be appreciated that various changes can be made withoutdeparting from the spirit and scope of the invention(s).

What is claimed is:
 1. A composition comprising a viral nucleic acidtarget sequence hybridized to (i) a non-radioactively labeled nucleicacid comprising one or more sequences derived from Herpesvirus saimiri,(ii) a non-radioactively labeled nucleic acid comprising one or moresequences derived from a virus related to Herpesvirus saimiri, whereinsaid related virus has at least 50% nucleic acid sequence homology withHerpesvirus saimiri, or a combination thereof, wherein composition ispresent in a human cell in an isolated clinical sample.
 2. Thecomposition of claim 1, wherein the viral nucleic acid target sequenceis a Herpesvirus saimiri viral sequence.
 3. The composition of claim 1,wherein the viral nucleic acid target sequence is a nucleic acid targetsequence of a virus having at least 50% nucleic acid homology withHerpesvirus saimiri.